Hi!
Our younger son had the lowest ERA and highest K's in our area, but his team never won a district game. He even lost a no hitter. In the end, it really didn't matter. To this day, all he remembers about his senior year is the fun he had playing with his buddies. He eventually was drafted by the Cubs and went on to pitch in the Big 12.
Try to help your son focus on his friendships, team goals, and the bigger picture. If he's throwing well, playing tough competition, and has a good attitude in the midst of adversity he will get noticed.
Stay positive and everything will fall into place.