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.
EDIT: Looks like Reddit created subreddits as early as 2006, so there goes that theory: https://en.wikipedia.org/wiki/Timeline_of_Reddit
Also relevant: https://techcrunch.com/2013/05/18/the-evolution-of-hacker-ne...
Choose the right tool for the job.
A subreddit might solve someone's problem, but to a first approximation it is never solving the problem of the person who coded it up. It is not a Reddit software engineer's passion project.