Very often. Air Force range safety guidelines require a million dollar flight termination system and most of that cost is testing and quality control. I don't have an authoritative list of all flight terminations but it happens at least once every few years whenever a rocket fails to follow the set flight path.
I also have to suspect things like isolated, dedicated and redundant comm links with the flight termination system are part of these guidelines. Perhaps even a "dead man's switch" that terminates the flight if this separate communication system loses signal at some point. (Even if this means a costly false positive or two~)
For the Space Shuttle, the flight termination system had two huge 10KW transmitters to send the signal. That would get through despite damaged receiving antennas, noise, or jamming.
As an example, the strut failure in the falcon 9 a while back didn't explode from the failure, that was the flight termination system that actually caused the fireball when things started going south.
