I have never done it, or heard of anyone doing it, and managing the database directly is not supported by the vendor of UBB.threads (as it is not using the built in tools for managing PMs). What you choose to do to your own database is entirely your choice.
If the users entries in the "ubbt_PRIVATE_MESSAGE_USERS" table are purged and a orphaned PT tool is run it should catch any messages which no longer are linked to any users.