Custom inventories are purged nightly? Uhm.
Take a look at Settings \ Notification Server \ Resource and Data Class Settings \ Resource History to verify if purging is on and what the retention is. Look in the field under Custom.
A 12 GB database should not be an issue. Ensure there is proper database maintenance and sql server sizing is in place. Our multi SMP environments have MUCH bigger databases.
SMPDiag can assist with general questions about database health.
HTH