While most CCW holders are indeed law abiding citizens, I should hope no cop simply makes the assumption that they all are when presented with a CCW permit. When engaging in a stop of any person they should be alert for their safety anytime a weapon may be present.
The typical procedure is still to separate the firearm from the person in some manner. We don't tend to even ask for the CCW until after that has done. Now, there is always the possibility that the CCW holder might NOT tell an officer he is carrying, and the officer may never discover he is. Why? Because chances are the CCW holder is not doing anything that might subject him to arrest or search, and while the CCW holder is likely required to tell law enforcement he has a permit and is carrying, if he doesn't, the officer may never know. One problem with CCW permits - at least in my state - is that there is no central database and running a person will not find any evidence of the permit unless it's in the local city or county system and that specific database is run. I've never worked in a county with such a database, so I cannot be certain it exists anywhere here.
It'd be nice to get statewide systems for CCWs similar to driver's licenses. I have heard that in some states they are already like this ... in CA, I think Sacramento is still hoping to outlaw firearms so they don't want to invest in such a system.