Version 4.1 of vCenter Update Manager, the software feature of VMware being able to scan and apply software updates on ESX and ESXi hosts, vCenter Server, Windows and Linux guest and VMware Tools, will be the last version to support scanning and remediation of Windows and Linux guests and applications running inside the guest.
Taken from the VMware vSphere 4.1 Release notes at http://www.vmware.com/support/vsphere4/doc/vsp_esx41_vc41_rel_notes.html
VMware vCenter Update Manager Features. vCenter Update Manager 4.1 and its subesquent update releases are the last releases to support scanning and remediation of patches for Windows and Linux guest operating systems and applications running inside a virtual machine. The ability to perform virtual machine operations such as upgrade of VMware Tools and virtual machine hardware will continue to be supported and enhanced.
Personally I think the feature being deleted from Update Manager is not a big issue. None of my customers are using Update Manager to patch their Windows guests. In all cases Windows Server Update Manager is used. The ability of Update Manager to patch powered off virtual machines is a feature that will be missed though.
Read more at the Gestalt IT website http://gestaltit.com/all/tech/storage/guest/favourite-vsphere-tool/