Is it possible to jailbreak an iPad 2 (A1395) after updating to iOS 6.0.1?
This is no longer true; Both answers were written before evasi0n came out. Now it's more than possible to JB 6.x devices, in fact up to 6.1.1/6.1.2.

As for backing up, you don't need to back up Cydia - it gets reinstalled anyway. What I would back up are any manually installed (i.e. hackulous-type) apps you may have (cd to /var/mobile/Applications, then do a tar)