HS coach here as well. If your son has talent and comes across as mature and humble when talking to coaches he will be fine. Overall it is frustrating to play for a lesser team but there are so many things to get out of it than just baseball. The college coaches will know he plays for a bad HS team and they will want to see how he handles that obstacle - does he show up everyday ready to compete, how does he treat his inferior team mates, how does he handle the losing and things like that. It helps the college coach figure out what his mental make up is.
He can still land at a high level prestigious college program without playing HS baseball but is the lessons learned he will miss worth it?