There are lots of possible reasons why a game gets removed.
Abandonware and no clear legal situation about the owner. No One Lives Forever for example. You cannot buy this game new for that reason.
Legal issues about used assets, licences, other things and legal disputes. Even though some issues could be solved, it leads to the next reason. Only Up has some of these problems.
Stress. Some people do not want to be public and famous. Some viral apps went that way.
The developer has regrets about publishing the game. For various reasons. Flappy Bird was removed for such a reason.
Fake games and impostors. Less likely to happen on Steam, but depending where you find a game, it might not be the real one, and got removed. Some "demo" versions on a free platorm might actually be malware scams.
Lack of time and commitment. If you release a game, you are somewhat responsible for it. Some games here have disabled comment sections because of that. (And others have it disabled, because they are scams). Indie developers are usually more to the ground and approachable, so they might feel uncomfortable to give support for a years old game they maybe not even have source code anymore.
Embarassement or other reasons for not wanting the game to be known. There is this thing with the director's cut in movies. If a creator of a work is unsatisfied, they sometimes try to fix it and sometimes just move on. It is artists and there is this trope of a painter destroying his own paintings.
For releasing on Steam as paid and not on Itch, specifically, there are idiosyncratic reasons. Payments are handled not in a way on itch the same way as on Steam. It is sometimes not possible to sell on itch for a developer, for some reason or another. Remember, that while itch is US based, the developers and users are all around the globe. There are projects here, where you can even get a steam key with your purchase. Of course not releasing on both platforms can have all sorts of reasons. The most trivial can be, that it takes effort to manage several distribution places. And let's be honest, itch is a puddle compared to the steam ocean. A game can have thousands of reviews on steam and have single digit ratings on itch. I kid you not. This game here has 2.8k reviews on steam and 4 ratings on itch.
Of course there are counter exampels. This one has 2k ratings on itch and 5k reviews on steam.