Personally, I think usernames are needed because they give HN the personality that it has. There are some people you might disagree with constantly, but you still value their input. Without names, you might not understand where they are coming from. Maybe this is more regarding comments, but sometimes submissions too.
On the other side, there is social aspect - I know a lot of HNers just by their usernames here; knowing a little of the writer's context makes a comment more relevant and interesting.
Perhaps it's worth a short experiment? What if there were a way of identifying within a thread which comments were by the same person?