I've noticed that the .db-wal file of my script is significantly larger than it needed to be.

The script keeps roughly 20 KB of JSON data around (serialized array containing 300 often-changing objects) but the associated .db-wal file is now (after 400 GM_setValue calls or so) 30 MB large.

Please disable journaling mode or run VACUUM from time to time (if not already the case).