Sure I've used a SQL DB. A file stored in a DB is slower to load than a file on disk. This doesn't speak to indexing and cacheing that a DB might have (not to mention that DBs are usually way better machines than your desktop). Of course, you can apply these techniques to files on disk as well.
Yes, 'a file'. Just have a look into:
/usr/portage /var/cache/edb /var/db/pgk
Where i found more than 75,000 files in more than 12,500 directories... Actions like fopen() and dir reads take much more steps than fetching the info from a database. On the other hand, one can modify things manually with the current system. However.. :)
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