Just spitballing here, but how about if it was reactive armor? The cybernetic armor needs to sense the damage and react in some way. Perhaps changing shape to better absorb/deflect the damage. Hitting it with an ion would short out the sensing of the damage and make it so the armor can't react. Which turns the armor off.
Mostly the more I thunk about it, the less Ion+Cyberware=Auto Shorting Out makes sense.
I'm beginning to think that having Cyber should just make non-Droids susceptible to Ion weapons in the same way Droids are. Make things a bit simpler to my mind, no need to refigure dice pools when a Brain Implant goes offline, etc.