yes it is... maybe if there is a question word (like what) then you have to reverse the pronoun but if there isn't you don't have to (compare "you are a boy?")
Well, the 'czy' part makes it clear that in Polish it's a real question (if it was 'albo' or 'lub' it potentially could not be a question), and then we always require the real question word order.
Yes, 'czy' is not a question-word here but it's this kind of 'or' that really requires you to choose between A and B.
It's not always necessary to repeat an article in an either/or situation like this.
"Are you a boy or girl?" is how I translated this.