I think który would be a more exact translation for which.
What/Jaki = what bread, in general, do you like? What kind/type of bread?
Which/Który = you have to choose one bread from a group of them, for example in a shop
You're right. Strange that I didn't use this translation. I'll add it to my comment, thanks.
I translate this as 'which' as well. If you must use 'what', it would be 'what type'.
"Jaki" (and its forms) is the 'adjectival' "what" (what kind of), "jak" = "how".
Can this be translated as "How do you like your bread?" That is a very natural way in which we would ask.
No, this is asking what type of bread you like, not the way you like it prepared.