I don't think it's "run by" the YCombinator. If I recall correctly, YCombinator pays for HN costs, in exchange for 3 things: recruitment posts, YCombinator new startups posts, and having alumni see each others as orange.

It’s really only the plaintext styling that contributes to the humble appearance.

The tech behind the scenes is pretty advanced though, from what I've read. (At least compared to reddit, along with apparently pretty good bot detection and such.)