Personally I think hierarchical comments are the worst part of reddit/HN. They try to force a structure where there is none, and make it more difficult to navigate a discussion.
1. With hierarchical comments, you can't respond to multiple people. If you want to make an observation about the way a thread is heading, or point out a mistake multiple posters are making, you have to either (a) respond to the comment that seems most appropriate to call out (b) respond to the highest voted comment to make your post more visible or (c) make a seperate subthread to make your point (but risk your comment being ignored). With chronological comments you don't have to choose, you can do all 3 at the same point and your comment is just as visible as every other comment. Believe me, there are lots of scenerios where you wish you could respond to multiple comments.
2. With hierarchical comments it's difficult remember the context of a discussion. You always have the mental overhead of remembering what all the previous posts were talking about or risk having to scroll all the way up (personally I just use Ublock Origin's element zapper functionality to hide the comments I'm done reading to get back to the parent). On the other hand with chronological comments you always know all the comments a comment is responding to, and if your forum software supports backlinks you also know all the comments responding to a comment. 4chan has the best UX for this, you can click on any post link or backlink to open a post and then go through all of the posts that post was responding to or all of the posts responding to that post, and so on. No other forum I've used comes close IMO.
3. With hierarchical comments if you're halfway done through reading a thread and want to refresh the page you have to scroll all the way to the top and go through every comment to see if you've missed any newer comment (but I bet no one actually does this and just gives up). With chronological comments newer comments always appear at the bottom so you don't miss any part of the discussion.
You're right about the clutter but you can disable all of those, with avatars and signatures disabled the average comment takes up the same space as an HN comment.