One example: When I open this page here, in eww all comments have the same left margin and I have no idea what is a reply to what, but with emacs-w3m the nesting structure is visible.
Strange, I'm trying out standalone w3m right now and also don't get nesting. Maybe the emacs version is different. I'm guessing HN must indent with CSS (which w3m pointed out it does not attempt to support) even though the comments are in a table.