There are many reasons why this could be the case, only one of which is naked self-interest on the part of YC to promote itself somehow. For example, it could also be correlative: YC funds interesting companies; HN covers interesting companies; thus you would expect that HN covers YC companies frequently.
Hipmunk was not just "a failed startup shutting down"; it was founded by a YC alum, as you note, but it was also design-focused with a distinct UX, good at PR, taking a somewhat combative approach in an industry popular on HN, etc., etc.
Most of that 96% of business do not have even one or two of those things?