My iPod icon has disappeared as well, but I assume the use of 5 icon dock in cydia is what caused it.
I did a complete restore, updated to 4.1, waited for everything to sync from my last backup, and the iPod icon was gone. I can still get to it through the multitask bar, the search menu, or voice activation, but the main icon itself is gone.
I'll probably do a complete wipe and try it again.
I had been using the 5 icon dock for the 5 features i use most on the iPhone.
Phone
SMS
Safari
Mail
iPod
(in that order on the dock)
I had a feeling this might happen and moved the phone icon out of the 5 icon dock before i did the final backup/restore/upgrade, but the icon still disappeared, so I'm not quite sure if the previous jailbreak or 4.1 is responsible.