As with anything, be reasonable. If you're really interested, then use whatever content is available to educate yourself, be it comments, the article itself, or independent research.
Further, I use https://theoldreader.com to subscribe to the RSS feed, makes all my "monitoring" a lot easier.
I think in many cases, the system comes down to "upvote the topic and comment if I agree with the premise (or what seems to be it), or downvote the article and comment if I disagree with the premise (or what I think it seems to be)"
I mostly rely on top level commenters replying to the article content, often with quotes, and then go down into discussion from there.
For the last group, the votes and number of comments are just signals for how good the link is - they don't care about the comments.
Probably the difference for me is that I live in Europe so I tend to catch up to a bunch of posts from the evening/night in the US during my morning coffee and then open hckrnews.com again by the end of the afternoon when some new posts begin to crop up.
I'll read the articles with interesting headlines but always jump to the comments first, some articles that I really think could help me in the future (or deserve further reading or research) I will save to my todo-list or in my Pocket account and then set a reminder to re-read/research in a given day when I'm free.
http://www.daemonology.net/hn-daily/ (HN daily top 10 links archived since 2010)
https://hnews.xyz/ (HN with thumbnails -> deeper HN skimming)