YC alumni see each other's usernames in orange. That plus the job post on the front page are the two YC-specific things that HN has. Both have been in place for a long time, and moderators try to be meticulous about not giving special treatment beyond that. (I say "try to be" because no one is the best judge of their own biases. But we do try hard, sometimes to the point of overcompensating.)

I don't think the colored usernames affect voting ring activity much. YC alumni and startups certainly are not exempt from the penalties we put on such activity, and frequently get hit by them. The first thing we always tell YC founders is not to solicit upvotes for posts because that backfires.