@Unknown It will not disable them, the emulator can read both zip and 7z compressed files. If you have scraped the games already you could run into a problem with emulationstation looking for whatever-your-game-is-named.ngp instead of whatever-your-game-is-named.zip (or .7z) which can be solved by rescraping or editing the gamelist.xml for neo geo pocket.
[edit: realized I worded the first sentence very poorly...]