Why I still use mutt:
I just tried to delete 16,000 messages in thunderbird, and had to wait 5 minutes for it to move them to the trash.
While I was waiting, I opened a shell on the same machine, opened a copy of the same 500-megabyte mailbox in mutt, ran a command to delete all duplicate messages (D, ~=, enter), and quit mutt (which writes out the modified mailbox to disk). This took approximately 20 seconds.