You don't even need to engage in that debate at all. Github doesn't allow porn on its platform. It doesn't matter what kind of porn (not the least of which porn that's illegal in the United States, which isn't Github's decision to censor or not). Github says "no porn," so no porn. Why does Github say "no porn?" Because their business model is to be a place where folks can do work, which necessitates it being a place where you can browse documentation without coming across NSFW content.

> because our advertisers/payment processors don't like it

Or, more simply, because if Github fills up with porn, the business professionals paying money to host their code on github will find a place that's not full of porn to host their code. It's a weird argument to say "Github's ability to make money and stay in business shouldn't matter because I want to host my awesome list of anime nudes."

> Like, in Japan, that kind of stuff seems, if not totally normal, at least acceptable enough to be included in stores along with other regular manga. So how should enforcement 'on the internet' reflect cultural values?

Github isn't a random store in Japan, it's the equivalent of an office building in Japan (whether you imagine it that way or not). If you brought your porn to work in Japan and hung it in your cubicle, it would almost certainly be frowned upon.