Itch is a self-publishing platform.
When you create a project page and publish it, that page can be seen by people who can then buy, download, or play your game.
The problem lies in visibility. People can find your project if they have the link, either because you provide it or because they see it elsewhere, like on Google. Many people use Itch's internal search engine to find games, but the dilemma is that Itch doesn't show you all the projects created within the platform.
If your project appears in Itch's search results, it's said to be indexed. If your game doesn't appear, then it's not indexed.
For example, if you go to https://itch.io/games now, you'll see "(1,343,636 results)," meaning that Itch's search engine has that number of indexed games, but in reality, it has twice as many games created. And if you search, for example, for all games that are "FPS," it will only show you the games that are indexed.
Being indexed helps people who use Itch find you more easily, but Itch doesn't index all games.
If you're not indexed, your page is still public and can be visited and promoted, but you simply won't appear in Itch's internal search results.
Another term is "quarantine." Quarantine occurs when the algorithm detects something wrong with your project and decides it could be harmful. In that case, anyone who tries to download your game will be warned. Unlike being indexed, which simply means you don't appear in Itch's internal search results, being in "quarantine" is an active measure that alerts your users that Itch believes there's something wrong with your game.