I'm late on this one, and haven't posted in awhile, but this is probably worth chiming in on. (Posted above anonymously, just replying in full here.)
I chatted with him after the fair, and also chatted with his parents for awhile. He understood the theory behind and around his work, and by all accounts did the work himself; this wasn't a parent doing it for him. What he did is likely going to save lives.
I also had a chance to talk to Nicholas Schiefer, who did a project called Apodura; better search of short content based on markov chain modelling. He also very much understood what he had done, how it worked, what some of the pitfalls were, and what he might do on it next.
Or, in short, at least at the level of winner/runner-up, they've done the work themselves, and are phenomenally advanced students. If you have experience in the target field - which the judges do! - it should be *very* evident which students have done the work, which students have done the work with assistance from a university lab, and which students are essentially parroting knowledge that a parent handed to them. Students that do phenomenal work on their own and can speak intelligently about that to a subject matter expert, I'd certainly give the benefit of the doubt.