Genética no universo parece seguir a genética do mundo real.
Todos os exemplos que você lista seguem o traço dominante de seus pais:
Jon Snow:
Parents are Lyanna Stark (mother) and Rhaegar Targaryen (father). Lyanna had dark hair (dominant) while Rhaegar had silver/blonde hair (recessive). Jon has dark hair.
Tyrion Lannister:
Parents are Joanna Lannister (mother) and Tywin Lannister (father) (yes, they were cousins). Both parents had blonde hair. Tyrion had blonde hair.
Alternate theory: Parents are Joanna Lannister and Aerys "The Mad King" Targaryen. This is a popular theory because Tyrion's hair color has been described as closer to silver, which is a trait of Targaryens. However, this would not affect the genetics, as both parents would still have the recessive trait.
Tommen Baratheon:
Parents are Cersei Lannister (mother) and Jaime Lannister (father). Tommen is not related to King Robert, despite having the Baratheon name. Both his biological parents have blonde hair. Tommen has blonde hair.
Além disso, lembre-se, de uma perspectiva fora do universo, de que os atores podem não ter o cabelo ou a cor dos olhos exato que seus personagens são descritos como tendo nos livros.