Unfortunately I, too, have seen the misuse of the Deleted Items folder as storage. Users assume, incorrectly of course, that if they need to retrieve the item again, they can use the Retrieve Deleted Items tool. As we all know, that cache does not hold mail items indefinitely. Every time I've seen this I've given my forehead a palm-slap and wanted to bang my head against the wall.
As for mailbox management, we've removed that headache. We limit our users' mailboxes to 100MB. We have the server automatically empty items older than 14 days from the Deleted Items folder, and we set up an archive to run every 7 days moving all items older than 1 month to their Archive folder which is stored in their home folder on the network. Yes, it does create a little more work for us when setting up a user's mailbox, but it saves us headaches in the long run.
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