I would suggest reviewing this Forum Topic, which another Admin had a similar question:
If the link below doesn't work, go to the Domino 8 Forums and search for the Topic "Deleting replicated mails from server mailbox" posted on March 6, 2009.
Overall, you want to be very careful of simply deleting files from the Server and entrusting users to maintain the databases.
Please feel free to reply with any questions as I do tend to check back in the Forums often.
I hope this helps Tien!