Hello,
This document is for the Symantec Endpoint Protection 11 and not for your Symantec Endpoint Protection SBE 12.
Did you say, "Removing the Network Threat Protection module from the SEP, then Symantec Protection Center just shows all the clients as disabled rather than showing whether their anti-virus software is up to date or not."?
That seems to be a Bug in the Software and Symantec is already working on it. Check the symantec knowledgebase Article below:
Client Endpoint Protection Status is "disabled" on the home page in the Symantec Protection Center when firewall is not installed
http://www.symantec.com/business/support/index?page=content&id=TECH123000
Hope that works for you.