Compared to a platform where only professionals publish their games, it happens very often in absolute numbers. I have personally seen it lots of times for lots of reasons.
It is too easy to create a project - and remove it. The circumstancial data is not telling why or what kind of projects. There are roughly 1 million projects on Itch. The unique counter is roughly at 3 million. So roughly 2 million projects were removed or never published. This would include things like unpublished drafts, updates by reuploading, removed scams, delisted items, and whatever other reason. It also does not tell if this was done by the developer or by Itch.
Removal of an established game is rather rare. Removal rate should be a bit higher than on Steam. There are some high profile cases known. One is currently happening.
For a use case like your's, and depending on how freely available those free games are, practically all games on Itch are without drm. So ensuring availablitily for the duration of an assignment should not be a problem. But that the same game or the same version of a game will be available in a few years is uncertain.
That last point might be more important to your case. Games change and this goes doubly for Itch, as you will find a lot of unfinished things and things in development here.
You might even contact the developer and ask for permission to use a frozen copy in school assignments.