Não.

The antagonists want the PCs alive--that's already been established. So let the players take a few runs at the guards; undoubtedly one time they will come up with something clever or amazing, which'll work. Let your players solve the problem for you.

(In addition, your players aren't actually aquele diminished by their lack of equipment. I cover that in "part two" of this answer.)

Why do we balance encounters?

Generally, we don't want to TPK unless the players ignore lots of warning signs and do actively stupid things. And we don't like a deus ex machina where the wires and ropes and assistants turning the crank are all visible. So we worry about balancing the encounter, making sure it's a challenge while ensuring player victory, and the game becomes about how few of their resources they can burn during any given encounter.

None of this applies here. Your players have a limited set of resources, but that's not going to stop them from making a big stink: the druid can still wildshape, the barbarian and paladin can still do tremendous--compared to an NPC's life--damage bare-handed (Divine Smiting left and right, literally!), but your fighter or rogue might be relegated to Helping the wizard make creative use of the one spell they have without material components.

Remember, the party need not kill too many NPCs before they'll run for help, allowing you to transition to a chase/escape scene. I mean, how many redshirts are really willing to die for their cause? Usually they don't have a choice, because we back them into a corner or gun them down from behind for XP. But this time the NPCs have plenty of 'outs,' and the players should be happy to let them use one.

And maybe the party fails, only to try again another day. It may feel a little like Dia da Marmota. But that's no insult--that's an awesome movie.

Your party:

You've added a bit of detail, so I will too =)

The tl;dr is your party is still well-equipped, even when unequipped, to handle themselves. They're down some ranged attacks, maybe. They're down a little damage output from the martials. They're down some AC, again mostly on the martial side, but you've got plenty of healing.

Há abundância of room for creative combat solutions with what's left:

As tuas clérigo tem acesso a Blindness/Deafness, Burning Hands, Calm Emotions, Charm Person, Chill Touch, Command, Cure Wounds, Detect Evil and Good, Detect Magic, Disguise Self, Divine Favor, Druidcraft, Faerie Fire, Find Traps, Fog Cloud, Guidance, Guiding Bolt, Healing Word, Inflict Wounds, Lesser Restoration, Magic Weapon, Mirror Image, Poison Spray, Prayer of Healing, Produce Flame, Protection from Poison, Purify Food and Drink, Ray of Enfeeblement, Ray of Sickness, Sacred Flame, Scorching Ray, Silence, Spare the Dying, Speak with Animals, Spiritual Weapon, Thaumaturgy, Thunderwave, Zone of Truth, all without material components. (Some might depend on domain.)

As tuas druida tem acesso a Beast Sense, Blur, Charm Person, Cure Wounds, Detect Magic, Druidcraft, Entangle, Faerie Fire, Find Traps, Fog Cloud, Guidance, Healing Word, Lesser Restoration, Mirror Image, Misty Step, Poison Spray, Produce Flame, Protection from Poison, Purify Food and Drink, Silence, Speak with Animals, Thunderwave, all without material components. (Some may depend on circle/land.) And they can turn into a bear! Or a mouse. Either might be very useful.

As tuas lutador can punch a dude and still do 1+STR damage, and can grab any ol' thing lying around to do an expected 2.5+STR damage. Assuming +3 STR that's still ~2/3 the damage you might have been doing be-weaponed. (That assumes same likelihood to hit--I like to give my fighters proficiency with almost any improvised weapon: the defining characteristic of the class is training with all types of weapons and combat, so I give them the most latitude with improvised weapons, too.)

Or they can Help their allies, or grapple, or shove... maybe this is the fight where the fighter não é the character to take the prize for damage dealt. That's cool, too.

As tuas paladino tem acesso a Branding Smite, Command, Compelled Duel, Crown of Madness, Cure Wounds, Detect Evil and Good, Detect Magic, Divine Favor, Ensnaring Strike, Find Steed, Hellish Rebuke, Heroism, Hunter's Mark, Inflict Wounds, Lesser Restoration, Magic Weapon, Misty Step, Protection from Poison, Purify Food and Drink, Searing Smite, Speak with Animals, Thunderous Smite, Wrathful Smite, Zone of Truth, all without material components. (Some may depend on Oath.) But you're probably better off spending those spell slots Divine Smiting with your fists.

As tuas guarda-florestal tem acesso a Beast Sense, Cure Wounds, Detect Magic, Ensnaring Strike, Find Traps, Fog Cloud, Hail of Thorns, Hunter's Mark, Lesser Restoration, Protection from Poison, Silence, Speak with Animals, all without material components. Actually, those don't look terribly useful. But you're a ranger, so you should be used to that.

As tuas feiticeiro tem acesso a Acid Splash, Alter Self, Blade Ward, Blindness/Deafness, Blur, Burning Hands, Charm Person, Chill Touch, Crown of Madness, Detect Magic, Disguise Self, Expeditious Retreat, Fire Bolt, Fog Cloud, Knock, Mage Hand, Magic Missile, Mirror Image, Misty Step, Poison Spray, Prestidigitation, Ray of Frost, Ray of Sickness, Scorching Ray, Shield, Shocking Grasp, Thunderwave, True Strike, all without material components.

If your party can't get out of jail with all of this at their disposal, let them sit another day and think about what they've done.

The sorcerer, druid, cleric, and possibly ranger and paladin will have access to some spells that don't require either a focus or material component, and the fighter, ranger, paladin, cleric and druid can use improvised weapons (chains from their cell, torches from the hallway, stools or their legs from guard stations, possibly even cell bars if one or more are strong enough to break some loose). To me, this means the party is only partially disarmed, though they won't have the full amount of stuff they'd be assumed to have at their level.

Solution: figure them to be one or (preferably) two levels lower than their actual level for CR risk calculations. Then apply some sense in how the enemies are equipped -- prison guards, for instance, generally wouldn't have missile weapons in hand during routine patrol; in fact, they might have clubs by preference over swords (their function is to maintain discipline, not to repel an organized attack). They'll tend to be cowardly; they have no reason to expect (or be trained for or experienced in) escape by leveled prisoners (vs. level 0 ordinary folk, who are unlikely to have the resources to escape unaided in the first place).

By the time the party finds their way out of the actual prison part of the "dungeon" they'll likely have found (most of) their confiscated equipment (at least the non-magical items). Finding the rest can be a decision they'll have to make -- but holy symbols and other foci, plus at least mundane proper weapons, will simplify adjusting encounters from that point on.

To explicitly answer your question: no, I don't think there is any inherent system or tool that will tell you what the new effective challenge rating of the party is now that they're devoid of equipment. You'd have to follow some other suggestions here and playtest through some encounters, or just guess.

To address the root of your situation, though, I would first jump to your implication that this will be some kind of combater encounter. I would sooner expect/encourage them to escape in some capacity - be it by force or cunning - and actively avoid combat. If they grab some inept guard through the bars and cause him to pass out, take the key, beat up a few more and poof, they're back... you're slowly cultivating a feeling in your players that they can't lose even when they lose. They lost a fight that got them captured, and the penalty is this prison scene. End of punishment, now back to the quest.

That's fine, I suppose, and you're the GM - you know your players and you know the group and in the end it's about having fun - but I think you have an opportunity to really make them sweat and flesh out their characters. Maybe they aren't given enough food over the course of 5 days and the evil overlord is seeing if they'll steal food from each other while he decides if he'll be adding any to his army. Or perhaps a slave trader comes by and buys one of them and then they have this whole new development while the fighter is hauled away by some guy with only one eye (whole new adventure!). Or maybe just the druid is wanted to see to it that these evil seeds germinate and the death plant of doom starts growing. Or algo. You have them out of their element. Do something with it! Don't just let them punch a guy and get their stuff back.

Basically, you need to work out how much damage the characters can do in this unequipped state, and how much damage it'll take to kill them. This is how most of the CR is worked out (it's more complicated than that, but at it's most basic it's based around average damage numbers). If they're attacking unarmed or with an improvised weapon, you work out the average damage number they'll roll (usually half the dice rounded up) and use that to figure out how strong enemies will have to be.

For example, if your fists/improvised weapons party can only put out X damage per round, and the party will be likely to fail once they've taken a total of Y damage, you balance the encounters so that the party is likely to deal that X damage before they recieve that Y damage.

If they can't heal up, you need to do this but spread the damage received over multiple encounters.

Playtest Encounters

If non-standard circumstances might disrupt the traditional, calculated difficulty of an encounter, the best way to determine a solid difficulty is through playtesting. Run the group through the encounters you'd like them to see, considering what abilities they might still be able to use without equipment. Fighters may be able to get an improvised weapon, while wizards may have a few spells they can cast without materials -- make sure to take these into consideration when you're playing and balancing the encounters.

Also consider the occasion that a player doesn't discover the options they have available: you can hint these options to players, or make sure that the encounters won't be too difficult without them as well. This should be an exciting escape, but not something that you'll want to kill your party with, as I can imagine it will be disappointing to die in a less-than-heroic situation.

Simple (or relatively simple) The party is not defined by their equipment, the party is defined by the party. Little skills the party might have can all come together perhaps the fighter has the strength to rip a bar off the wall while the rogue is clever enough to pick the lock, now they have a club and a way out. Maybe the party is going to act stealthy, not getting into a fight is still winning a fight but as stated a fight may be inevitable.

Balancing is a tricky issue and something I try to avoid if it makes sense for the party to be overpowered then they're overpowered but to say they can't get around this is preposterous, use this as an opportunity to let your party think and roleplay and if that isn't enough they won't be going without equipment, one guard gets unlucky and now the fighter is armed and ready to rumble. Now the next guard goes down even easier and the paladin can be armed now there are two tanks protecting everyone else until they can get equipped as well. Arm that cleric and you've got a three man wrecking crew ready to handle some low level guards. If they run into the big bad boss then not only do I not expect them to win I don't want them to win. Parties don't win every fight or else it gets terribly boring.

You could use a npc that would help the group just enough to get through the encounter with a posible chance of death if they do not play well.

Since the NPC wanted them incarcerated instead of dead, have the immediate monsters attempt to subdue them instead of kill them. If they lose, have the NPCs give them a cut that is an attempt to remind the "prisoners" that they are indeed prisoners. If they overwhelm the guards, have most of their equipment nearby, but maybe a key item has been taken elsewhere.