ZIP files cause headaches on some emulators that may or may not support the specific ZIP format that archive is in, so to avoid any ZIP issues I have unzipped ALL archives so that the ROM is there for the emulator to load without having to spend extra time extracting the ZIP archive to a temporary file then loading that. This all causes emulator slowdowns, even just a small one it all adds up, plus if you're using purely an SD card or USB pendrive to run everything from it will be even slower. Also an increased risk or SD card corruption with all those read/writes on an SD card

The only archives I leave alone are the arcade ones, these MUST be left zipped or WILL fail. MAME, FBA and NEOGEO are the main 3

I use OSMC with KODI and RetroPie so have it run everything from an external USB hard drive, the only function the SD card performs is booting the PI 3 B I use at the moment then control is passed onto OSMC which runs off the USB hard drive so being much faster and much less chance of SD card corruption. I know thats not possible for everybody especially if you have a portable RetroPie in a handheld where space is very limited