I also have one leg longer than the other. I've spent my entire life standing with all my weight on the shorter leg. This has caused scoliosis in my spine, and major pain in one hip. Go to an orthopedic doctor and get a built-up shoe for the shorter leg. I don't think it will be obvious to other people and it will save you from a lot of pain later in life.
Not at all, we naturally have one leg a bit shorter than the other, just not that much. He should still be able to run without trouble... unless he jumps with two feet when he runs... : P Hope this helps!