you are far more optimistic then I am - I would highly doubt that we are conducting any "extra" scrutiny on muslim applicants to west point - because that would be profiling. and its not politically correct to have that.
the bottom line is, these muslim applicants could well be AQ members (secretly of course, in the context of their private lives) - and we wouldn't have a clue.
You'd be surprised what we know. It isn't hard to track the history of an 18 year old kid. Especially one who must meet very high educational and extracurricular criteria. Not many teenagers can achieve a 4.0, score 1400 on the SAT's, become an Eagle Scout and student body president...and attend formal terrorist training at a Pakistani Madras.