Here, "what" means "which", standing as it does before a noun.
That's not quite the same as "what" which stands by itself.
Welsh has different words: beth is "what" (standing on its own) and pa X is "which X, what X" (before a noun asking to identify a particular such noun from a group of possible similar nouns, e.g. which colour out of those that exist or which book out of those on the table).
https://www.duolingo.com/comment/13404102 is probably a sentence you are thinking of?
I have the impression that sy is a relative "...which is", so there you have "what colour hair is it that is with you" whereas here it is simply "what colour is the little tortoise" rather than something like "what colour is it that the little tortoise has?" so it takes the normal "is" verb.
A long time after you were discussing this, but, trying to make sense of this myself:
I think 'sy' is used when the 'pa' or 'pwy' are the simply the subject of the 'sy'. 'Pwy sy'n siarad?' 'Pa liw gwallt sy gyda ti?' (what hair colour is with you?)
This crwban sentence is a different structure: crwban and liw are subject and complement of the verb - i think that's why it's ydy / yw not 'sy' here.
Croesawn i (? I'd welcome?) gywiriadau.