https://en.wikipedia.org/wiki/Hanlon's_razor
"Never attribute to malice that which is adequately explained by stupidity."
Exchange malice with intentional and stupidity with being overworked and swamped.
You assume this is intentional on Itch's side. It's not. They might intentionally delist something, but that is rather rare. And I will explain why your games are not listed at the bottom. But Itch will take their time, when something is flagged for staff review. And they will never talk about reasons. Even two months waiting time for regular indexing is not uncommon.
Does this suck? Of course. But your games are not inaccessible. You need to do your own promotion. Itch does not see itself as a platform like Steam that picks games and serves them to the users to maximize profit. It sees itself as a file hoster with attached shop and some features. Internal and passive promotion by being visible on the catalogue is seen as secondary. (I got that impression by various topics where leafo posted. My impression might be wrong.)
The moderator is a community moderator. Not staff. No time moderates these very threads you are posting. Itch has no tech support message board. Staff does not read here in general. For whatever reason they still made some communication channel, where the mod can tell staff a ticket number. But it is still staff doing the work, and that means, they are still swamped and overworked with things and even with that ticket number known, they might not work on that ticket any faster in some situations.
What did happen to your games and why? I can't tell for the past, but currently it is this:
The two projects are in quarantine. All quarantined games are delisted as a side effect.
Why are your games in quarantine? No one will tell you the actual reasons. Itch fights against malware. There is hundreds uploaded each week. They will not give a blueprint for how to more easily avoid the mechanisms they do have. Waiting time to get out of quarantine is about the same as for indexing. Maybe longer, depending on the reasons for the quarantine.
The games are still accessible, even in quarantine. There is just that warning message.
WARNING: This Page Has Been Quarantined
Our system has flagged this page for additional review due to potential suspicious behavior from the page owner.
If someone has asked you to download from this page and you don't fully trust them, or their behavior isn't what you recognize, then we don't recommend downloading this file until our team has reviewed the page.
Password-protecting files or pages is a technique often used by scammers in an attempt to block virus and other security scans from detecting malware. Do not trust password-protected files unless you fully trust the uploader.
Learn more about the "Try my game" Discord scam