Well it's not really a copy. You're just looking at the same emails that reside in the mailbox it searches. It's just a smart search folder that shows the emails you're looking for. The acutal emails remain where they are until you do something with them and you can do it from within the smart folder.
For quick organizational purposes, you can make different smart folders with different criteria to help you when you get a lot of email. Just depends on how someone would benefit from the uses.
It's true that you can't program a smart folder to perform a function such as move. It's really just a specific search tool that is always there until you no longer need it and delete it.
Deleting a smart mailbox will not delete the messages within, but you can manually select the messages within it and delete or move them to another mailbox and it will remove them from where they reside.
I'm sure you could use automator to perform an action automatically, but I'm not really familiar with using it to build a script. But without getting to complicated, it's not so hard to check that folder on occasion and manually perform the actions needed.