I see that the lr-caprice32 has support for m3u playlists - https://github.com/libretro/libretro-cap32 - so you can create a .m3u file containing each game's disks.
Emulationstation doesn't know - yet - how to handle those files and it will not show them, though. If you use the lr-caprice32, you can create your custom es_systems.cfg - see here) - and add .m3u as known extension.