I transferred my email contacts back from Thunderbird to Windows Mail then did a sync and it all went smoothly. I don't know of a way of doing it directly from Thunderbird, though. Maybe other Members will have some suggestions.
You'll probably have to transfer your contacts out of Thunderbird to a more well-integrated source (ie Windows Mail, as the above posted suggested), and then transfer them to your iPad. It's a bit of a hassle, but I'm not sure there's a way to do it directly.