I guess I could see where there might be an issue, but most everybody who's made the point about violent videogames is pretty much dead on: My sense is that most of the issues with kids and violence in games come from thoughtless, reflex-action gorefests, not contemplative, methodical games like SH3.
Not to say I don't appreciate many of said thoughtless, reflex-action gorefests, but there is such a thing as age-appropriate. Also, if this kid is that young and can get his head around stuff like manual targeting, it doesn't exactly sound like he's in danger of dropping out of school or anything.
