Hi,
Thank you for posting in Symantec community.
I would be glad to answer your query.
1) Is there a way via command line we can add file scanning exceptions for directories? I want to exclude from any form of SEP scanning etc, two directories.
--> No, it's not possible with the help of command line.
2) We have a managed site, and in the management console Network Threat Protection is OFF and Locked, and on the client I can see it's unticked and greyed out, however there are two users who are getting disconnected for 60 seconds every now and then during the day. Is there additional logging I can enable to determine the cause?
--> Check the eventviewer logs entries. You can run Symhelp tool to find out possible root cause if there any from SEP side.
http://www.symantec.com/docs/TECH170752