Full title that doesn't fit in the HN headline: "Mastercard deflects blame for NSFW games being taken down, but Valve says payment processors 'specifically cited' a Mastercard rule about damaging the brand" (For the people who don't click the link to read the article.)
There are definitely a lot of links in this chain. Maybe leafo can chime-in and say exactly what happened with Itch.io. But I suspect that someone downstream of Visa/Mastercard anticipated that the payment card companies would not permit the transactions and relayed that back up to the merchants, and they shut it off preemptively. But it's hard to say. Mastercard is now saying that they never said or did anything. So…
As far as I'm aware, the Collective Shout letter caused a "formal card network inquiry" to originate from both Mastercard and Visa. I did not have access to the actual inquiry, but my assumption is that it wasn't "we see this content, take it down" and more like "we saw this letter, look into whats going on before we do our own investigation and fine you"