Thunderbird does not delete messages, not even when you empty your trash can. Yes, the messages have gone from the program itself, i.e. you won't see them, but they are still there, lurking away inside the relevant folder in Documents & Settings (or wherever you installed Thunderbird to).
We found this out purely by chance when J wanted to import his message/account to one of this other computers; the deleted items folder was huge - but there was nothing to be seen when looking at the program. Ditto another folder that was empty to look at in the program was in fact fairly large in the folders in Documents & Settings.
We dug into the vast array of Help and FAQs and discovered it's all to do with Compacting Folders - to totally delete messages you need to run 'Compact Folders'.
If you want to do the whole lot simply click on a folder, then go to 'File' and select 'Compact Folders'. The bar at the bottom of Thunderbird will let you know how it is going and will tell you when it's finished. If you've never done this, it will take a fair while (depending on how many emails you get/delete). You can also compact a single folder by right clicking on it and selecting 'Compact'. There are a few add-ons as well, one that allows you to put a button on the menu bar - but that only lets you compact a folder at a time and for someone like me who has a very detailed tree structure, it's of no use. There's also one that is meant to be tied in with emptying the trash can, but try as I might I couldn't get that to work. So I do it manually. Also in 'Options' 'Advanced' 'Network & Disk space' you can set it to compact them when a certain amount of space will be freed up.
I've always stayed clear of the word 'compacting' because when I last used OE it meant 'I'll empty your folders and put the messages somewhere else on your computer'. Which is fine if you realise that's what it does, but not if you don't. But Thunderbird doesn't do that thing; the messages stay where you can easily access and find them - in the program.
Not compacting folders apparently, as well as having all this rubbish you thought you'd got rid of - which could include viruses even if your virus checker doesn't strip them out, but merely flags them up - just sitting on your hard drive, can cause problems with Thunderbird being sluggish or crashing.
As I said you probably know this, but in case you don't, I'm sharing the tip.