My question, is there an issue with comments I'm not seeing? Do the popular topics on the homepage have dozens of spam or troll comments that are pruned out constantly, so I don't notice the problem? Or is the issue those 1 or 2 downvoted comments I mentioned earlier?
HN receives a small number of comments, so fine tuning algorithms isn't a big deal in my opinion. This isn't Reddit, where the number one post right now has 4,000 comments. That presents a lot of complications, since they need to try and cycle new comments so they all receive some visibility, allowing them a chance to rise if they're of high quality. On HN, you have 20 comments, or 50 comments, so regardless of the sorting, nearly everything gets read. As long as HN generally sorts comments, they're fine.