I think it's just mistake. More people would check the job board if there were more jobs there. YC company jobs could just be sorted to the top automatically to give them a leg up.
This is a really good point. Being the only ones there decreases the YC companies' prominence, because unless people are specifically thinking, "I want to be an employee at a company backed by Y Combinator," they're probably not going to check there very often.
https://hackernews.hn/user?id=whoishiring
and look at the submissions. Beats crawling through results on searchyc.com.