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Higher frequency will reduce noise, but increase losses on switching transistors. Have no idea which motors and drivers do you use, byt 31 kHz was choosen because human's ear not hear them.
The lowest possible frequency such that audible noise is not an issue will result in least eddy current and noise levels.
Keep high impedance signals very short and avoid current loops, and stray LC coupling.
Make sure you have excellent grounds , shielding and CM ferrite filters where needed.
Probe using very short leads or just tip & barrel for signals < 50ns = Tr
I recall hearing portable power drills with motors in the early days around a few kHz, but many better designs now are silent.
If PWM is poor for noise and higher impedance when switch is off then consider going to full bridge VFD design with low impedance throughout mechanical cycle, but monitor current for limiting loading and changes in speed.
There are sometimes advantages to using fairly high frequency PWM for some things, but driving a dc motor is not one of them.
As you say, the speed cannot change instantaneously, so there is no loss of control sensitivity.
Switching at a low frequency has advantages from the efficiency point of view, and there will very likely be fewer potential problems with designing the electronics.
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