Most military aircraft do not appear on flight tracking sites for secrecy reasons. Even if they are on innocuous missions, they are not visible on public air radar maps.
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MILITARY Flight Tracking and History - FlightAware.
Websites such as ADSBExchange.com, FlightRadar24.com and FlightAware.com aggregate flight data in the United States and abroad using a mix of commercial and citizen-owned sensors that capture the movements of commercial, civilian and military aircraft in real time, 24 hours a day.
Generally, aircraft requesting that they not be displayed on Flightradar24 are military aircraft. Some military aircraft, such as various transport aircraft, are visible.
Tracking military planes presents special challenges (but is not impossible). In the United States, regulations facilitate anonymous flights by private jets. And in many parts of the world, ADS-B coverage is limited because of a lack of receiving stations.
When VC-25A or the currently under development VC-25B are in the air but not carrying the president, air traffic controllers may refer to them by their tail numbers, Special Air Missions (SAM) 28000 and 29000, or by a call sign of their choosing.
Blue: Aircraft displayed as blue icons are currently being tracked via satellite. Satellites are collecting the ADS-B signals from aircraft and transmitting them to the Flightradar24 network.
Why do military planes not show up on flight radar? The main reason is that they want to protect their security and avoid detection by potential enemies. Military planes often fly on classified missions or sensitive areas that require stealth and secrecy.
The position is calculated based on many different parameters and in most cases it's quite accurate, but for long flights the position can in worst cases be up to about 100 km (55 miles) off. In settings there is an option to set for how long time you want to see estimated aircraft on map.
The most well know of these is the code 7700. This is used to indicate an emergency of any kind. A pilot will enter this when in an emergency situation - either instructed by ATC after declaring an emergency or without communication if there is no time.