@battlecat One way to do this would be to do the following:
Scrape all of your roms to make sure all are listed in the gamelist.xml file.
Manually edit the gamelist.xml file (usually located in ~/.emulationstation/gamelists/<system>) to remove the unwanted roms.
From the main emulationstation screen, push start, then find the option in the menu that says "Parse gamelist.xml file only" or something like that.
Reboot your system, then enjoy!
This is how I hide the various bios files as well. Of note, if you add a new system or rom, you'll have to disable the "Parse gamelist.xml" option to see the new roms, unless you've scraped them already.
Good luck!