Reddit is also pretty "ugly". I put the word in quotes on purpose, since both are very functional and clean. On the other hand, they definitely don't have a particularly beautiful design, as most designers would tell you. They're enough for what they do, but they don't make you say "wow, what a beautifully designed site". That's my opinion, plus (I think) a common consensus among HN users.
ugliness is also about functionality and not only style, and IMHO there are a couple of usability aspects in HN which which can be considered as problematic, just from the top of my head:
1. lack of search
2. "expired links" when clicking on "more", without any description of what is going on
3. "expired links" when you are commenting and take much time to submit your comment
4. no hints during comment reply saying whether there are any formatting rules/conventions which can be used (like quoting, lists etc)
5. no possibility to do comment preview
I agree that at least for some of these there is some rationale behind, but still it's far from being "simple because perfect".
