I don't see a problem for him provided his throw ends in pronation and not supination which is the usual scenario.
However, I do see a risk element for the player receiving the ball as in a double play or, especially, a tag play. Side arm throws tend to break and the last thing an inflelder receiving a throw wants is a breaking ball.
If his career is nearly over I would leave him alone since it would take a lot of time and effort to change him and only then if he was willing. But if he has the talent and desire to move up the ladder he must get this throwing error corrected before HS.
Generally the more side arm he will throw the more pressure will be put on his elbow, but in turn the more upright his motion will be the more pressure it will puts on his shoulder. Completely overhand is usually taught as the "correct" motion since shoulders usually hold up better than elbows. A bigger factor to his arm's well being would be how he does his warm up exercises and stretches. There would be no problem as such but in case he feels stress on arms or shoulders then he must consult a chiropractor.