If I understood it correctly, they’re not talking about a chip literally running at 50Mhz. They’re talking about polling a sensor in a loop running on a 50Mhz timer. The processor doing that is certainly running at a much higher clock frequency
Yeah they're talking about the control loop itself which means 50 times a second the computer/program looks at it's inputs (sensors) and changes it's outputs (commands to actuators). The actual computers processing that program run much faster.
That's the number of times per second the main update code runs and it has nothing to do with the number of clock cycles or instructions per second the CPU can run (other than the fact that the chip needs to be fast enough to have the update code finish before the next time it needs to start).
Chips have internal timers which can be configured programmatically so they emit hardware interrupt in specified time intervals. When the interrupt is emitted, CPU jumps to the method which executes the certain program. After that it goes idle, waiting for the next cycle.