I think that this is because syntactically they are on the same level. Assuming I'm reading the source correctly, they're all cells in a table, at the same level, rather than being nested.
So elinks et al. are correct; the site is using CSS to indicate something not in the structure.
Interesting. I just tried reading HN on Firefox Mobile recently, and noticed that the comments all show as on one level, not nested. But show okay in mobile Chrome.
I still think using Elinks of w3m creates a more streamlined experience if your end goal is getting work done.
That's probably because HN uses HTML rather poorly (from the point of view of HTML representing the semantics of the content.)