Yes, deleting the roms/files in the folders will hide the emulators but if you also want to hide cavestory and/or the input config screen you will need comment them out in es_systems config.
Here is commands that will allow you to do this, along with backup your old one:
cd
cd .emulationstation
sudo cp es_systems.cfg es_systems.cfg.bak
sudo nano es_systems.cfg
Then add a # infront of each line you dont want. Ctrl-X and save when done.