If my son plays outside and exercises, does it matter for his health if he plays videogames when he's inside?

That depends. The american academy of pediatrics reccomends that kids have no more that 2 hours of non school based computer+tv+video time per day to preserve normal growth and developmental progress. Excesses are known to eventually create problems with weight and classroom performance. Social skill development requires interaction with real kids, not just words on a screen.
All in moderation. There's more to life than school and exercise. Mental stimulation, social interaction, and building of life skills are too. Media with violent content, as most video games are, can alter how the brain functions, desensitizing youth to violence and inappropriate behavior. Brief periods on video game systems playing non-violent games are fine, but should not replace other activities.