You can beat down an OPCOM to a level where they will toss everything they have at your forces to kill you. Then if you beat that they will significantly slow down to the point where you have effectively beaten them into submission if you are running them set as occupation or invasion. I don't know about Assymetric as we haven't done many of those missions.

The way I understand TRACE is it is more along the lines of an intelligence gathering system that you can set to update every so often (in minutes). It is more of a tool to use rather than a function of what you have done. While it shows green that means you have eliminated the threats that were there but depending on how you have the OPCOM set they can and will return to the area in an attempt to retake/clear it of you and your forces.

As for the profiles all over the map many of those are virtualized. Those profiles are not able to be seen until you go drop in either as Zeus or as a player. Go take a look at the link here to see what it means; it is a really well written description on profiled and the Active Limiter.
Virtual AI System Wiki page