This is not that uncommon. If you are lucky your son has teachers who love him anyway and will write good recommendations. If your son is creative, funny, especially insightful a good essay may give him a nudge. But mostly you should be extra cautious and assume that he may be judged on his grades more than his scores, so make sure you find safeties and matches that he likes.
Sometimes kids like this flourish in college where they can take mostly courses they like. Sometimes they crash and burn as the lack of structure proves impossible to deal with. I’ve known a number who ended up on waiting lists, so senioritis can be especially problematic for this crowd.