There is no tool as such, but this could be an excellent job for the Database Tool.
If you use the CLI, look in dbconfig.json for potential databases, otherwise look in the UI under “Database” for each job.
You generally don’t need the databases in there, except for active backups (the Duplicati-server.sqlite file is special). The databases are just an index of the remote storage.
If you accidentally delete one, it can be recreated using the “Repair” command.
If you no longer have the backup data (the .dlist.zip files), then the database has no purpose.