In the end, I've decided to use SQlite for metadata. It seems to be as fast if not faster than e.g. libmysqld, and it has a really simple clean C interface. According to benchmarks, it should be way more than fast enough to suit my needs.
For larger data structures, I'm planning on just storing them in separate binary files (the SQlite website says it can store binary data, but that if your data size exceeds a certain amount it is faster to store it in flat files instead - see this page).