Yes. "y" as an adverbial pronoun can also be used in questions. Of course, as in other types of sentences, only to refer to a place already mentioned.

I have found one example of your specific example in a article of a French newspaper (Le Figaro):
"Ensuite si vous faites un référendum, qu'y mettez-vous ?" - Then if you do a referendum, what do you put in there?