Yep, maybe when any given registered user uploads a file for the first time, some variable should be triggered to mark this user as elligible to show in your Manage Users screen.
I think you can deal with it with just using a mere usermeta value: if defined, the user has uploaded files.
And when all her uploaded files are deleted, the usermeta value may be deleted, thus hiding the user from the manager. A basic semaphor. That’s what I’d do. Not really sure if it’s too difficult to implement.
Or… you can simply check if there are files to show in the user’s folder. The only problem with this, is that if you have hundreds of users WITH lots of uploaded files, you can generate a high IO usage everytime that screen is loaded, even taking for granted the use of results pagination. That’s what I prefer the usermeta value in the db, you just cache the value whenever it changes and that’s it. And given that it’s an on/off value indicating if there are files or not, it shouldn’t change very often. ??