The MP3s would only be hidden if you transferred them in MTP mode and then tried to view them in MSC mode.
If you always use MSC mode, and still cannot see the files, it’s possibly because you’re looking in the wrong place.
The database indexing on the Clip+ gets artist/album/track info from the ID3 tags in the MP3 files.
MP3s which have missing or incomplete ID3 tags will be listed under " Unknown".
Now maybe the Clip+ firmware should use folder/file names in that situation to guess the missing details, but it simply doesn’t work that way.
I think there’s an assumption that if you’re just playing legitimately obtained music, it will be tagged correctly already, and if you’re playing something else, you would know enough to tag the files yourself.
I agree the database refresh is too slow; on 1MB and 2MB devices, it didn’t matter too much, but when people have 8GB Clips and 16GB μSD cards it’s a nuisance.
I only update 3.5GB of files once or twice a week, so I can live with it;.
Rockbox on the same hardware doesn’t take as long to create its database, so maybe Sansa’s own database indexing was never intended to handle large numbers of files.