What are the implications on vibration measurement from decreasing Pulse-Width Modulation (PWM) frequency of a 9V electric motor?
It's all about frequency.  If the PWM frequency is within the range of frequencies you are measuring, then it will very likely show up as a spike in the measurements.  If it's not, then it won't.  It would be smart to arrange the PWM frequency to be past the range of vibration frequencies you are trying to measure.

Fortunately, that should not be hard for normal "vibration" measurements unless you are doing something unusual.  Usually you want the PWM frequency for driving motors to be in the 25 to 50 kHz range anyway, mostly to minimize current ripple.  At that frequency, you can think of the average current as producing the torque, with the ripple being AC that does nothing useful to drive the motor.  The AC component only causes heating against the resistance of the coils.

Keeping the PWM frequency above 25 kHz has the added advantage that it is above the audible range.  Generally "vibration" is even lower in frequency, so the desired signal should be easy to separate from the PWM noise.