I researched about this and even asked my hosting provider, but they didn't give me an answer.
I am paying for a Softaculous license in a VPS.
I used it some time ago to install WordPress and NextCloud.
But I disabled the auto-update for both since I want to do that manually.
I want to remove Softaculous, because I am not using it anymore, but I wonder if that will have any effect on the already installed apps.
My hosting provider tells me to "just do it and see what happens", but I don't think this is the cleanest way to do something.