Yesterday I did my experiment with the help of some jelly beans (thanks mom for the suggestion!). I sat Hughes down and asked him "are you a girl or a boy", he answered boy, I asked " do you want candy or a kiss", he answered kiss so I gave him a kiss. I told him if he wanted candy then he needed to say "candy". We went through boy or girl with him saying the correct answer, we did what's mommy with him saying the correct answer, etc.
All in all, I would say my experiment was a success and I got the positive results that I was looking for! I learned that Hughes does know he's a boy and he's just not that interested in answering my questions when candy is not involved.