I assume you're talking about upgrading because of MMS. The carrier profile will most likely come without a firmware update, meaning you won't lose your jailbreak when you get MMS.
However, to answer your question, no. You cannot backup Cydia apps on iTunes. You have to manually download each one again. Make sure you copy them all down so you don't forget to redownload any. But for any apps you paid for outside of the Cydia store, your serial number was copied so you won't have to pay for the app again. For any apps you paid for in the Cydia store, it's linked to your Facebook or GMail account, so you just have to log in there and you can download it again.
