Nexus S 4.0.3 (OTA) missing icon in the phone app
Are you sure that that isn't the way it should be? Today I recived a 4.0.4 system update for my Nexus s. Try updating yours from 4.0.3 to 4.0.4. 

Edit:
That is the way its ment to be. Me and many people I know have it like that. Where did you get the first image of the dock bar from?