My school had closer to 400 students per grade than 1000, but it still had pretty defined cliques that people categorized into nerd/jock/popular kids/whatever. Additionally, bullying was still common, it was just mostly non-physical.

Regardless, even in this thread there are people who claim to be from small schools and have not experienced physical violence. I'm not saying it doesn't happen, but I do think it's far, far less common than Hollywood would have you believe.