Most of my post are really long but I make this one short.
Try to switch your core, emulator, to a LibRetro one. They have better support in my opinion.
You might have over looked this because most if not all games when used are in Zip or 7z format. You never mentioned if your games are using a 7z or a Zip extension, for N64 on Batocera only the LibRetro emulators allow use of Zip and 7z file extensions or archives in general..
I know the non-LibRetro ones Mupen64 emulators looks better and go full screen but N64 games are giant in size especially when talking about roms.
Go into the menu, I think space bar on a keyboard is the default and change the N64 emulators to a libRetro one and try your roms out.