Or is it "now you have thousands of applicants who would have never joined if YC didn't required it." (sic)

For clarification, per PG:

"The first thing I notice when I look at an application is the username it was submitted under. If it's one I recognize for making thoughtful comments on Hacker News, I give the application extra attention."

http://ycombinator.com/howtoapply.html

So I can fully understand that while joining HN is not a dejure requirement to getting accepted to YC it certainly seems like a defacto requirement based on the above statement.

No one's complaining "too many usernames are taken"; people are complaining about the comment quality.

When you get a HN username to make a YC application, you're going to be hyperaware that you're here visiting pg's home turf. You'll either try really hard to post high-content, insightful comments, or you'll simply lurk. Either way, you're not likely to be wandering around urinating on the furniture.

tl;dr -- the requirement seems more likely to boost, rather than harm, comment quality - if it has any effect at all.