Not all version control systems use the filesystem.
In fact, one such distributed version control system, Monotone, already uses SQLite for storage. The FAQ Why an embedded SQL database, instead of Berkeley DB? gives some rational for this choice. The FAQ doesn't address "why not filesystem storage" though.
Even SVN, at least historically, supports an alternate BDB repository data-store. While this is not SQLite it is easy to imagine that SQLite can function as a "super" BDB that supports SQL as an interface. (Actually, BDB can even be used as an SQLite back-end, for a fee :-)
Keep in mind that, no matter where the data (diffs/deltas) is stored it all ends up as some form of "BLOB" -- BDB value, data in a file, or BLOB column in a[n SQLite] database.
Happy coding