Ninja does use some database-like things, but they are just in a simple text/binary format. It's actually been long enough that I have forgotten the details.
https://ninja-build.org/manual.html#ref_log (contains a hash of the commands used) / https://ninja-build.org/manual.html#_deps (database-like thing with some mtimes, see https://github.com/ninja-build/ninja/blob/master/src/deps_lo... )
The sqlite3 database used in redo was just something I threw together in the first few minutes. sqlite was always massive overkill for the problem space, but because it never caused any problems, it's been hard to justify working on it. I'd like to port redo from python to C, though, and then the relative size of depending on a whole database will matter a lot more.
Ninja isn't too big though. It looks like about 13K of non-test code, which is great for a mature and popular project. Punting build logic to a higher layer seems to have been a big win :)