Yes, if you unlocked and jailbreaked using Pwnage on any firmware 2.x, when you use the iTunes updater to update to 2.1, it will remain unlocked (but not jailbreaked).
So if you want to use Cydia apps, you should use Pwnage to jailbreak 2.1.
If you don't need to use Jailbreak / Cydia apps, then you can just let iTunes update the phone.
Mine is using the official 2.1 firmware on T-Mobile USA right now.