I'm assuming disabling the outputs will also cut power to the stepper drives?
If it doesn't, the drives will remain in fault until the power is disabled.

VFD wise, cutting power is fine, provided the power is cut cleanly, however the spindle could still continue to run for a few seconds afterwards depending on how quickly the internal capacitors discharge to the point the VFD faults out due to under voltage. The easiest option is to have the forward/reverse/run disconnect instantly, which they should do if they're wired to PMDX outputs, but also have the input power cut at the same time. That way the VFD should have things stopped, before it runs out of power.

From a practical point, there should be no noticeable difference between using a common +5V or common 0V/Gnd.
The main thing is to use suitable wiring to eliminate/minimise noise, which could cause lost/gained steps.