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.
“iTunes 9 plays well with already-jailbroken and unlocked devices”
“@JonathanCee @VictorBissou yep it’s safe to update iTunes if already jb/unlocked. Just don’t update iPhone firmware too!”