Strong shoulders, especially posterior shoulders, help stave off the dreaded shoulder injuries... like SLAP lesions.
There is no way you should drop overhead strengthening, as long as proper shoulder mobility is maintained and proper attention is paid to the posterior shoulder especially external rotator cuff muscles.
That said, most of throwing power comes from using the hips, and the arm like a whip much like you would use a catapult or trebuchet.
Strengthening the hips and making sure he has correct technique is all important. Tim Lincecum on the Giants is a perfect example of a kid who throws extremely hard whos not heavy. Watch his throwing mechanics.