Hello!
I wouldn't worry at all if I were you. I have a long family history of pectus excavatum, including myself. I have two children who do not have this though. My grandma, dad and all have/had this as well as two of my uncles. My grandma lived to be 93 and my dad is very healthy this day, as well as myself and my uncles. The only things we've really experienced, that has been attributed to this, were short episodes of our hearts racing. The first time I experienced this, that I know of, wasn't until high school. It raced for a minute or so and went away. I have had EKG's which were inconclusive. I was told not to worry about this and this happens to many people and can be a one time thing.
I was and continute to be very active, in every kind of sport and activity you can imagine, without any sort of a problem what-so-ever. I actually didn't even know I had a "problem" until later on when I realized my friends didn't have this same indent I had. It's tricky for females, as you can imagine, fitting certain garments on top!
Anyway, I wouldn't think any problems would lie in your son's future at all - let him be the little boy that he is without limitations! I hope this is encouraging for you and your family!