I agree with you re: academics. I don’t think it is necessarily bad that he is held back a level for A+ at NYSSMA now, though maybe only being close to the situation could judge it. He is only a freshman, after all. I remember going with an ensemble to NYSSMA my senior year and scoring 100 out of 100, but our instructor and performance were indeed very high caliber. At any rate, you’ve got time on that.
It may be a little difficult to balance, but it sounds like you may also want to continue pushing the well-rounded academic strengths with regular school teachers and curriculum, as well as excelling in the percussion program. Since he is still young, you could also potentially look at additional percussion / music instructors down the road, if you feel there is somehow an unbalanced approach taken by the current instructor. It is hard to discern from my end.
Editing to add: while it is true one must excel in the audition for top conservatories, that is no excuse to cut back on academics. Plenty of other instruments achieve just that balance, and for a percussionist so young, I don’t see why it is any different. Top percussion can have a bit of a ruthless focus to it, but if you son already does well in academics, there is absolutely no reason why he shouldn’t also continue to do well. I would also be a little suspicious of an instructor who couldn’t allow a young musician time for his studies.