I've been doing this for the past two months with great success.
Caveat: Don't hibernate/sleep on one OS and boot into the other and launch Thunderbird. What a mess.
With that out of the way, it's actually pretty easy to do.
I created a small 10GB FAT32 partition that serves as my go-between for whatever I want to shuffle around, and to store my Thunderbird data. I still have misgivings about Linux writing to NTFS, so I felt the shared partition was the way to go.
With Thunderbird succesfully set up with an active message store on either side, stop Thunderbird, go to the .thunderbird folder (either in your Linux home or Windows "Documents and Settings" structure), and edit the Thunderbird .ini file. There's a use-relative setting that should be set to Y, and a path setting to point to where you want your message store - adjust to suit.
Then, copy or move the message store under some funky-gibberish named folder to your desired shared area. Launch Thunderbird again to verify it sees your email, and you're set for that side.
Boot to the other side and repeat the process.
It's worked quite well for me, even with a half-gig mail store.