Some food for thought on #1: I've been in the military for 14 years and do a lot of Anti Terrorism training. We're still being taught to remain inconspicuous on commercial flights just do what a hijacker says. On a personal (and logical) level I would want to be as close to the cockpit as possible to prevent a hijacking.

6: I'm also an air traffic control radar technician. Any plane can be tracked without a transponder. Air traffic control computer systems build "tracks" of data from reflected RF (planes), the transponder data from the plane (flight number and a couple other items) is associated with the radar track. If a plane turns off their transponder the track is still there but associated transponder data is gone. An alert air traffic controller would then try to establish communications with the plane to find out who they are and what their intentions are. They might make a manual change to the track and put it in some kind of "unknown" category. Transponder data is basically a "nice to have" feature that makes and air traffic controller's job easier. Anyone can change the info the transponder is transmitting or turn it off completely, RF still bounces off big pieces of steel flying through the clouds and a radar doesn't care if a track has transponder data or not.