Ainda não há uma resposta canônica para isso, mas me deparei com uma hipótese interessante por u / mrzoink em < um post href="https://www.reddit.com/r/StrangerThings/comments/519y04/how_are_the_lights_manipulated_from_the_usd_world/d7akucu"> r / StrangerThings no Reddit:
Speculation: Joyce psychically reached out to Will, through an interface not entirely unlike the one Eleven uses, a CB radio. Both are electrical audio devices. Will was at "close range" which we can assume helps. Will only breathed on the first call - he didn't say anything, because he didn't know Joyce was hearing him.
There was a second call. Joyce managed to reach out to him this time, but only barely. She managed two way communication.
Joyce is able to do this because either she has some previously untapped psychic potential, or because everyone has some capacity to do so and the events of the series make this easier (the rift, the monster, etc.), or because there's some special connection because of the mother-son bond.
Joyce intuits that a complex interface like a phone is too much for her ability, or the situation.
Will only breathed during the first phone call. Most likely he was not using the telephone in the Upside Down at all, because if he was he probably would have said something. The second time he hears Joyce.
When they use the Morse code light string ball, Joyce tells him how many blinks for yes, how many for now. She is getting better at the cross dimensional communication.
There is probably no interface at all on Will's side.
She's speaking directly to Will's mind, but only if he is "close."
The alphabet wall is probably a variation of the same thing.
Will might be growing in psychic ability during this time too.
Taking into account the episode 8 scene with Jonathon and Joyce sensing each other across dimensions, the thing that is common to Joyce / Will and Joyce / Jonathon is Joyce.
An alternative theory would be that Jonathon simply guessed, but Joyce definitely sensed him when Jonathon said "mom."
Another theory would by that the Byers boys are both (somewhat psychic), another that all the Byers are psychic, and finally a last one that everyone has psychic potential.
P.S .: Todos os créditos vão para u / mrzoink ; Apenas citei as partes do post que são diretamente relevantes para essa questão.