Community building and maintanence is a very tough job, and the simplest of things can end up nudging people towards unproductive behaviour. HN has consistently maintained at least a decent quality audience and community by keeping the UI free of bells and whistles, and thusly being unattractive to certain kinds of low-effort users. At this point, any change would probably count as messing with a good thing, so the thinking is probably "if it ain't broke, don't fix it."

They are however acknowledging some things that are broken and need fixing, and in recent days have been introducing small changes to correct those (eg. the unvote button, ability to fold). I do hear you on the notification for comment replies thing though, I was really surprised when I found that feature wasn't there, and at times end up missing out potentially good conversations because I didn't check for and notice the reply comment until too late.