asbesto, this is what I did:
I opened my FTP client and connected to my PI. in /home/pi/RetroPie/roms I created a new directory called _unused * and then I moved all direcotries(=systems) that I don’t need into the _unused directory (e.g. atari, n64, msx, etc.). that’s it. there is no need to change any config files.
alternatively, I could have deleted all directories, but this solution seemed to be more appropriate since if I ever want to put up some N64 or Atari stuff onto my PI, I simply move back the belonging folder and don’t have to worry about how it was called.
* the _ prefix is simply to have this directory stay on top in the roms directory when I connect via SFTP to transfer stuff