I still don't get it much (not a web developer). The only customization that I see is probably in the top bar. Can nothing be done that the page contents are still loaded from the cache but the top bar is loaded separately and customized for logged in users?
Sure, it can be. You'd either need to cache the portion without the top bar (so you still need to generate some HTML), or load the same page for everyone, and then do an AJAX request for the top bar, for example. Each has its pros and cons.
Both of these increase complexity though, so they may not have done either.
Complexity shouldn't be that big an argument for a large and influential site like HN. Adding partial template caching is not that complex, definitely not for silicon valley haxx0rs.