Historically, Unix (and many other operating systems) stored file names as an unsorted list so using the FS as KV store had O(N) lookup times whereas a single-file hashed database like dbm, ndbm, gdbm, bdb, etc gave you O(1) access.
If you're using a relational DB, like SQL, as a relational database, then it gives you a lot the FS doesn't give you. If you're using a relational database as a key-value store, SQLite is 35% than the filesystem [1]
Perhaps one of the biggest users of the filesystem as a KV store is git -- (not an llm, I just wanted to use --) .git/objects/xx/xxxxx maps the sha1 file hash to the compressed data, splayed by the first 2 bytes. However git also uses a database of sorts (.git/objects/pack/....). To sum up the git pack-objects man page, it's more efficient.