There's a college thread that touches on this. The conventional wisdom is that "If you hit, you will not sit", and for that reason the ability to play multiple positions is a plus.
In HS, it depends a lot on the program. If freshmen always play on the freshman or JV team, a talented player like your son should get a shot to play, and coach will likely slot him where he has the most potential. On the other hand, if your son plays at a school where one or two of the best freshman generally make Varsity, your son's ability to play multiple positions could be a real advantage. By looking at who graduated last year, and who remains, you can probably figure out where the team's needs are greatest, and your son can try to get reps there and prove he can contribute.
The one thing to be wary of is being the 2nd or 3rd best catcher on a team. That kid usually ends up catching a lot of bullpens and never seeing the field.