Nope, Nate ends up with neither Serena nor Blair. The books are totally different to the show, it doesn't affect the shows couples at all. Chuck was gay and had a monkey.
Uh, actually, in the books Chuck's bisexual... a bit different to gay. He's basically the same man whore as on the show, but ends up with a proper boyfriend. & he doesn't have much to do with Blair at all. & I'm pretty sure Blair loses her virginity to Nate. (= I just totally spoilt it.