Updating to iTunes 9 Does Not Affect Jailbreak or Unlock
MuscleNerd from the Dev-Team says that it is safe to update iTunes to iTunes 9 even if your iPhone or iPod Touch is jailbroke and/or unlocked. So, if you have a jailbroke/unlocked device… go ahead and updated iTunes. However, do not update to firmware 3.1 via iTunes. We haven’t heard anything official on the 3.1 firmware update and how it affects jailbreaking and unlocking yet. We will keep an eye on the Dev-Team for more info.