I published 11 games and I had indexing issues with 3 of 'em. Initially they were indexed, but a modification in the page has removed 'em. Once I complained of it in the forum (or Reddit, I don't remember) and tried to modify the page again; the games were indexed again. I'm not sure if modifying the page could cause an indexing, but you could try. Itch.io staff should watch every single non-indexed game and approve it manually, but I don't think they have the time to do that at the moment, because of the new NSFW policy.
I have your same problem and if my last game will remain deindexed for a week, I will try to modify the page again.