So droids cybernetic upgrades are shut down only when the droid is shut down (from too much Strain, probably caused by ion weapons), while meatbag cybernetic upgrades are shut down when first hit by a ion weapon.
If this is correct, I think it should be specified under the Droids "racial ability": this one could be a major "power compensation" for their low stats.
Yeah, I'm not exactly crazy about that bit either, though the fact the ionization blaster doesn't actually have the Ion trait (instead it has a Stun Damage entry that only applies to Droids, and by extension cyborgs), though Ion is noted as being having those weapon "fitted to ships to knock out opponent's shields, sesnors, and engines." (pg106)
As for Vader, who's to say that his cybernetics weren't specifically upgraded to be immune to the effects of ion damage? It was an upgrade option presented for cybernetics in Galaxy at War, and it'd make a certain kind of sense to have the Imperial Badass-in-Chief protected from something as piddly as ioniization effects. After all, he'd seen first hand what sort of thing could do to a battle droid, so he'd at least be aware of the risk.
I also re-read the drawback paragraph regarding cybernetics, and it says that "if hit by weapons that normally would affect only droids, the cybernetic enhancement temporarily stops working for the remainder of the scene or until repaired." The next sentence says that "the consequences of this depend on the enhancement in question, and the exact details can be left up to the GM." So going by a strict reading of what's printed, just getting hit with an ionization blaster disables the enhancement, with the full extent of what the consequences of having that enhancement disabled means being in the hands of the GM.
Personally, I'm thinking that "enhancement disabled" should simply mean that if you're receiving a bonus from your cybernetics, such as a +1 Brawn from a Mod V cyberarm, and take damage from getting shot by an ionization blaster, you lose that bonus, but the limb itself would still be operable. Alternatively, the bonus is lost and the cyborg suffers a setback die to all actions involving that cybernetic upgrade until repaired or scene ends. Either one is much less punitive than "cybernetic is shut-off, sucks to be you." If the only cybernetics you have are prothestic replacements (like Luke's hand in ESB), then you might get the setback die, but that's it.
Ion Weapons, being Vehicle/Starship scale for the most part, would probably drop most characters anyway, so that's a bit of a moot point as the only Ion Weapons currently listed would deal 80 points of character-scale damage, so cyborg or droid, you're going nighty-night if you get hit with one of those.
I do agree the cybernetic upgrades could use a second look by FFG, both in terms of how they interact with droids (perhaps making it clear that droids don't have them disabled if struck by ion-type weapons) and meatbags (does the upgrade really become totally useless, or is just the bonus lost, or some middle ground between the two?). Also, modification option (even if it's just as simple as doubling the cost) to make one's cybernetics immune to being disabled by ion-type weapons.