The 'N' number is a bureau number not a 'squawk'. It is registered on the flight plan. Squawk is assigned by ATC, with your IFR clearance. 4 numbers. Military/Gov't don't have to squawk (use Transponder). Most do because you want to be an identified track for flight following, traffic separation etc. Most of my time I squawked 1200 (VFR) or had the transponder on standby (on but not sending). But most of my time was 500' or less.
When AF1 takes off either an E2 or an AWAC goes up or is already up. They are the ones calling bogies or targets or whatever air traffic is going on. They don’t need an identifier so the question is why the N/A? Which doesn’t make sense unless you aren’t the President so not allowed to identify as such. The whole thing is screwy. Because if the President is on board they identify as AF1. Not N followed by a number. If the President is not aboard then they identify as the N plus numbers. Same deal wth the chopper.