As voting based social communities become more popular, the more nuanced commentary get's drowned out by the popular viewpoint. The issue isn't the site being "too mainstream", the issue is that the nuance gets lost amongst the noise with social voting. I'm not sure if it is because of the appeal of the popular viewpoint itself, or if it is because of the amount of posts containing it.
Reddit 10+ years ago had, what I consider, great commentary on the default subs/frontpage—it was very different than the Reddit of today.
"Good" social voting sites get more popular with time; I agree with you and think it's almost inevitable that HackerNews will too. My philosophy on this is to just enjoy the site while it's in the state of popularity you like, and try to find a new one when it happens. Yearning for yesteryear isn't exactly productive. ('Better to have loved and lost than never to have loved at all'?)
My take: HackerNews is still quite niche in comparison. I'd estimate the comment volume is one or two orders of magnitude away from the point where it becomes too noisy to find the nuance.