@Zing I'm using a RPi4 booting from a SD card, ROMs and other system stuff stored in a 32 GB USB stick, fresh install of RB 7.1.1.
When using a MAME folder without any subfolders, the Arcade virtual system shows these ROMs as expected, together with FBNeo (and NEO-GEO, if enabled) so this problem looks like an unforeseen consequence of using subfolders... There is an option to display subfoder contents when in the Arcade menu, but it didn't help.
Nevermind about the Naomi ROMs, the documentation only mentions MAME and FB in the Arcade virtual system, so it probably won't apply to other cores/emulators.

@acris ok)

still looks like you can't set date and time according to the ntp server that was defined