Like many systems, DBMail is optimised for efficiency and forgiveness and requires occasional maintenance.
The maintenance app is dbmail-util and regularly running this is good practice. The -a flag checks for message integrity, body/header/envelope cache check, sets the delete status for deleted messages, purges deleted messages, and cleans up the database. If for example you wanted to keep all deleted messages you might run the app without the -p purge flag.
Database schema upgrades are automatic from version 3.
Normal database monitoring and maintenance are outside the scope of DBMail, see the respective documentation for more information.