The subject isn't really used in questions; when it is it's usually put at the beginning, e.g. "Tu quante mele hai?", and sometimes at the end after a comma, e.g. "Quante mele hai, tu?". Putting the subject in the middle is common in some dialects though, e.g. Florentine ("i'che tu fai?", what are you doing?).

My understanding is that youre making a statement ("tu hai") followed by a question ("quante") and theyre conflicting. In English you can say "you have HOW MANY apples?!" to express incredulity, but i dont think it makes sense translated literally into Italian.