I first tried to create the same situation with Mail.app but then noticed, that the dock icon only counts the number of new mails in the inbox and ignores my other folders. It was also quite a pain to get the Textmate mails (the mailing list with around 16,000 mails for me) into its own folder. Still, even after doing this, even the Textmate folder (which has roughly the same amount of mails in both clients) was way slower in Mail.app than it was in Thunderbird.
Another problem was, that the internal spam filter had way too may false positives. I'd say nearly 400 mails got marked as spam while being ham. Yet another problem was Mail.app's stability. The moment you run a rule on a mailbox containing n*10^4 emails I guess you can start getting some hot beverage and pizza. I went to my favorite in the meantime (for about 2 hours) and the process appeared still to no be not finished :-(
That said, I still would like to have some kind of AddressBook.app integration for Thunderbird and a fast maildir implementation would also be great, but I think, for now I will simply keep making huge backups everyday and be happy with Thunderbird ... and hope that Thunderbird 2.0 (apart from getting more attention by Mozilla.org after the release of Firefox 2.0 next week) will offer some nifty new features that will help me in my decision making next time :-)