Reddit was great when it started. It gradually diluted.
HN was opened to the public, who then had access to already tight and information-dense conversation started by YC members. HN was, at that time, some of the best, most focused, highest signal-to-noise conversation one could find on the open Web.
Usability is in good part determined by the users. In addition to the length of time involved since its inception and initial tweaks to appearance, there is the matter of what the core HN population was and, I hope, continues to be interested in: Communication. Getting knowledge and ideas across. Sorting the most valuable (as determined by the community) to prominence.
HN continues to do pretty well at this.
And even in its graphical design... Well, the Verdana typeface was developed by one of most prominent type designers, for Microsoft, to be particularly readable on-screen. (Admittedly, screens at the time were still mostly CRT's. But even with LCD's, for quite a number of years the dot pitch did not change all that much.)
Text is nice and black. It's on a light gray background rather than white, to reduce eye strain.
Just because it doesn't look like a highly customized version of Bootstrap version whatever, doesn't mean it's not good at what it does.
I have seen complaints about usability on mobile devices. Overall, I think this simply hasn't been enough of a concern, nor considered to be having enough of a negative impact, for pg and crew to take it on.
Also, realize that any number of site and design decisions may and I suspect are made without any publicity or acknowledgement. pg and moderators fix problems and determine optimizations, and some of these depend upon a lack of publicity.
It might even be that pg doesn't particularly want the influence of "momentary" attention in conversations. Enhancing mobile usability might be viewed as contributing to a decline in the quality of conversation and/or voting.
I'm not saying this is happening. But I am saying that, with respect to some aspects of the site, sometimes you have to read between the lines if you're seeking the why of it.
Unlike reddit, there has been no private messaging facility on HN. pg has stated, IIRC, that he didn't want to / see the value in putting the effort into developing one. But... the decision might also be viewed as lessening the avenues for "submarine" conversations and the development of cliques.
He did support a third party initiative for notification of responses to comments. And your profile does allow you to state means of contact outside of HN. But there's a bit more friction in those means, and perhaps to good effect.
Finally, pg has stated repeatedly that -- in what started out as a side-project that was specifically YC focused -- he puts the effort he does put into HN where he thinks it adds the most value. E.g. comment quality, spam and destructive participation whack-a-mole, etc.
Not that pg needs me to speak up for him. But, to state what I've observed from my perspective and so perhaps contribute my bit to overall efficiency, here.