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.