Some high profile aircraft, such as Air Force One are not displayed. Most other aircraft subject to restriction are shown as anonymized by aircraft type.
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Military aircraft in particular are exempt from many civil rules and regulations which would see most aircraft having an active transponder and of course their operational requirements will dictate they often do. That said, ultimately, any plane CAN disable it if they wish.
And while the plane features a private residence, meeting rooms, a medical facility, and Secret Service agents, there are no weapons onboard. With an essential role of transporting US officials, let's look at how the Boeing VC-25 can thwart any attack despite being unarmed.
They are almost as tall as a six story building, and they're as long as a city block. Each has four General Electric CF6-80C2B1 jet engines, which provide 56,700 pounds of thrust a piece. The top speed is between 630 and 700 miles per hour and the ceiling maximum (how high the plane can fly) is 45,100 feet.