Have you edited or deleted much content? Files in the contentstore are only ever created or deleted but never modified - editing a file (whether via the Web Client, CIFS, FTP, WebDAV, APIs, wotnot) always creates a new file in the contentstore, orphaning the previous version (assuming versioning is turned off). Files that are "orphaned" in the contentstore (due to either edits or deletes) are not physically deleted until 14 days (by default) after they become orphaned.
Deleted files are even more tricky in that deleting a file actually moves it to a kind of "Recycle Bin" (the deleted items area), and unless a user (or the admin) cleans out deleted items regularly, the deleted files will continue to hang around in both the repository and the contentstore indefinitely (consuming disk space in the process).
Cheers,
Peter