I’m not sure what you’re asking, are you saying your microwave oven does not emit any sounds that you can hear?
My microwave emits a completely unbearable fan noise and I have to be in a different room if it’s on for more than a minute or I feel nauseated and angry. Maybe your cat just doesn’t like the noise, like me?
I’m saying that, in addition to the fan noise, perhaps it’s emitting some noise that is beyond my range of hearing but that is driving Kitty up the wall.
Do you have power settings, which cycle the microwave magnatron on and off? If so try it on the lowest setting (defrost is one such setting, about 30% power). You should be able to hear the magnatron on-off cycle, perhaps 10 seconds apart. You can see if your cat is just effected when it’s on (cooking cycle) or just the fan and turntable running.