There can definitely be problems with imbalanced muscles around a joint. Many times it is the front of the shoulder girdle being stronger than the posterior side. If muscles are imbalanced it can definitely put the shoulder in a bad position. Its important to strengthen both sides of the body in the weight room. Many pitchers posterior shoulder girdle muscles are much weaker than the anterior girdle. You can sometimes see what is called winged scapula. This is when the rhomboid, mid-trap, and serratus anterior muscles are weaker. You will often see the shoulder "rolled" forward instead of being back in good posture. These can both lead to shoulder and elbow injuries.
A physical therapist that I have worked with some and I really trust has a website that describes some of this. I think the website is www.posturalrestoration.com. He traces a lot of problems like this back to the hips being out of balance and then everything from there up has to compensate. I bet that if you would look at your son's shoulders, his throwing shoulder is lower than his nonthrowing shoulder. There are several things like this. It kinda sounds a little bit out there but I've seen him work and I think its pretty amazing. Someone like him might be able to describe more online or in writing, but I only feel comfortable giving very basic information about what he does.
In summary, there can definitely be problems with muscle imbalances. Almost everyone has some types of imbalances but many times they don't manifest into further problems. Check out that website and he has some pictures on there that show how to check for imbalances and what to look for. I hope this helped you somewhat.