You're missing two important facts: first, that your pending comment eventually (after 24 hours) expires of its own accord, and second, that you can always delete the comment if it's taking too long and holding you up on a better comment you could have written.
In reading a thread (say, over the course of 5-15 minutes), I will often want to post comments at various points. Because I am not in a popular HN timezone, if I needed to wait for comments to be endorsed, I would find this seriously frustrating. Waiting and checking to see if a comment had been approved would be a huge time sink.
Edit: I think that limit has been lifted to five now.
