I really can't address the why, because I don't know, but I can give reasons as to why it's a good idea to keep them separate. Y Combinator is motivated for a

I really can't address the why, because I don't know, but I can give reasons as to why it's a good idea to keep them separate. Y Combinator is motivated for a variety of reasons to have a place like Hacker News, that is not ultimately controlled by another company, so they actively maintain and moderate it. Users are motivated to go to a place with a particular common denominator. The common denominator base is broadened when the forum is nested in a larger forum. Sub-reddit moderators have to take active steps to keep their users a specific subset of people, this extra effort also has the side-effect of excluding people who don't fit the criteria who may positively interact. Keeping HN separate from Reddit makes it easier to balance these competing interests. Also, a great number of people like compartmentalizing to various extents for various reasons. A monolithic entity makes this more difficult.