Let's assume that HN is a terrible place where sexism and racism are easily found--consider that the ability to review people's posting histories is a really good datapoint of figuring out whether or not they're somebody you want to work with. If an applicant applies with a posting history rife with sexism and racism, then maybe they're not going to be asked back. It's a chance to let people show their true colors, and many people are bigoted shitbags.
So, even looking past that, the author raises the point that YC has a portfolio north of 30B USD. So, erm, maybe whatever they're doing is working? Maybe, just maybe, sexism and racism and everything else is not really that relevant to running a successful business. I don't want to go full libertariloon on this and go claim that the free market thus proves those are non-issues, but from a business standpoint they don't seem to be mattering. A criticism of "but but but imagine how much better things could be if they stomped it out!" is a non-starter, because it's playing in what-ifs.
If HN does have a problem, it's that the downvote system is bullshit and broken and enables people to hivemind more easily. PG screwed up, in my opinion, when he gave a blessing on giving downvotes based on disagreement instead of civility or relevance. The moderation system is opaque and broken, though much less broken thanks to people like dang.
Mostly, I think, the single systemic issue of HN is that people are not self-selecting for good technical content, and are so closed-minded that useful discussion of non-technical content becomes boring, tedious, and prone to flaming.
EDIT: Thank you whoever gave that downvote without explanation for helping to demonstrate my point!