First, 92KB is only a tiny portion of the phone's storage. That's 0.0000092 of the phone's storage.
Second, disabling the app doesn't do anything but keep you from using it if you want to. File Manager doesn't run by itself, and there's probably no app that you use that allows you to use File manager to choose files, so disabled or not it's just going to sit there. But if it's disabled, and you ever have to go looking for a file (say a picture or a song), you won't be able to use File Manager to do it - disabling it hides it from you.