Not cool having thousands of files. Too much reliance on the underlying filesystem. Having a single database file would be faster, easier to export, easier to manipulate, and more robust.
XBMC/Kodi does use a single SQLite database for metadata.
I assume you are talking about NFO and image files when you say "thousands of files"? If so, those are completely optional. They simply serve as a sort of backup and/or way to load custom data into the database. Once scanned into the library, those individual files are no longer used.
XBMC also fully supports using a mysql database which can be remote on any machine in the network. It allows different instances of xbmc to share library status