With discrete control panels located in the cockpit, within an arms length of either pilot ... the power for the systems originate at the circuit breaker panels, which obtain power from aircraft power systems and distribute it to the various systems that require it.
The control panels also direct control signals to the remote transducers themselves, perhaps through a black box, thereby controlling transponder functions remotely ... in other words: that transponder system is located somewhere within the fuselage, perhaps at the tail, which is controlled by the control panel in the cockpit, with power coming from aircraft power through a circuit breaker, as it is distributed through the circuit breaker panel.
If someone wants to 'shut it down', they could 1) flip a switch at the control panel, or 2) UN-power it at the circuit breaker panel by opening the related breaker, or 3) disrupt the power between the circuit breaker panel and the black box or transponder itself by cutting a power wire, or, 4) disconnect the transponder connectors at the tail, or somewhere else in the circuit along the way ...
Some aircraft systems are designed to be controlled in a 'fly by wire' system, which uses a multiplexed control system that could be controlled through radio signals from the ground ... I do not believe that transponder control would be involved in such an arrangement ... and as far as I know, no such accommodation exists ...
So yes, that system could be disabled in a number of locations ON THE AIRCRAFT, but it is unlikely it was disabled remotely .... the most feasible method would be, flipping power switch at the control panel, or opening the circuit breaker to cut off power to the transponder system
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