Sadly, Digikam does not let you put your database in a separate location to your thumbnails database. This is sad because you typically want your database on redundant storage (e.g. a RAID-1 mirror) for safety, but the thumbnail database is just a cache. Fortunately, you can fix this yourself with a simple symlink:

$ mv thumbnails-digikam.db /fast/ $ ln -s /fast/thumbnails-digikam.db thumbnails-digikam.db

... where the /fast directory is on an SSD or similar fast storage.