On 2, I prefer it the way it is. If I want to go to the Hacker News index, I can click on "Hacker News", which is, after all, right there beside the YC logo.
A person might go there to find out things about YC. I mean, supporting YC is the ultimate purpose of the Hacker News application, after all.
In any case, YC is not a separate site: it's the parent site of this application. The logo is not the Hacker News logo, it's the YC logo, and should link to YC.
No, I'd argue that they are separate sites, though it is obvious that y combinator is affiliated, and it's linked at the bottom of the index page. Very rarely will users of hacker news want to go to ycombinator.com, so having the link in such a prominent position is a mistake.
