/var/spool/qscan/settings_per_domain.db is created with /var/qmail/bin/qmail-scanner-queue.pl -p. Thats assuming you're actually using per-domain/per-user settings in qmail-scanner of course. If youre not, you can just ignore that message in your logs.
Whenver you make changes in qmail-scanner.ini, you need to rerun qmail-scanner-reconfigure