NFL scouts -- at least some that I've spoken with in the past -- care about character. I've had scouts call me and ask about what some players are like, if they've gotten into any trouble, if they're good kids.
So yes, they're paying attention to what's going on at North Carolina. The college careers of Marvin Austin, Greg Little and Robert Quinn are over, but their futures as professionals are not. While the NCAA rulings aren't likely to affect their status as football players, questions about their character might be tough to overcome.