I was poking around on my drive today on my linux box trying to account for 2Gb of space in use that shouldn't have been. You can imagine my surprise when I found that Mozilla had kept a copy of every email message it had seen since March! The short story is, Thunderbird doesn't actually delete the messages when you move them to the Trash and then empty the Trash.
Details on how to make the messages really get deleted from your drive are found
here.
Boy, what Einstein thought this was a good idea?