By default it puts them in the Trash folder. That's what it does on my system.

But in doing so, it may well be following the Deletion settings for each account that you find in the Account Properties under Mail Management.

If you want to be sure, I'd recommend that you create a few duplicates by copying some messages (drag+drop with Ctrl pressed down) to a preferably empty folder and then move them back (drag+drop) to the source folder. Then use the Maintenance Center to clean up the duplicates and see if they end up in the trash.