The funny thing is that HN doesn't even adhere to the basic UX practices that many around here constantly complain about in new design like knowing what is clickable.
Take a look at each story list item on the front page, what do you think is clickable? Everything in the subheading is formatted exactly the same, but not everything is clickable. Same goes for the headings of each comment in a thread. And I think HN's violation of this is especially egregious since the formatting of these things aren't just the same, but they are greyed out. That's a pretty universal sign that something is not clickable. This is 100% confusing to new users.
This one is a bit more difficult to implement without a lot of JS, but one thing that I have run into many times is reading through a comment thread, trying to reply, realizing I'm not logged in, logging in, losing context of where I was, scrolling through the thread trying to find where that comment was, giving up and not commenting.
In addition to that, not remembering which comment threads have been collapsed. Accidentally navigate away? Good look finding your place again, especially if there were many new comments added.
The mobile experience can be summed up as "very precise clicking"
I think the top menu items are also named in a weird manner. Why does comments take you to a list of random comments in chronological order? How is that useful? You would expect that link to take you to your profiles comments, but no, that's the "threads" link. There is a lot of that on HN where things are (imo, purposely) obscure. I get why they would do it, but let's not pretend it's a good experience.
HN caters to the most technically literate community on the internet. They will figure out how to use this site no matter if you had to navigate the site via the terminal (some would probably prefer that "NO JS!"). We've all gotten used to how the site works, we ignore all of its issues because we've adjusted our habits to work around those issues.
And I'm not saying HN has terrible UX (there are actually many things we can learn from it) but it's definitely not the site I reference when I need inspiration for a good experience.