You could houserule it, making augmented character very vulnerable to electrical damage, but as written the cybernetics are not taking electricity damage. The character is. Because cybernetics don't have their own physical condition boxes, they aren't vulnerable to taking matrix damage from an electrical attack.
On the one hand, it's kind of cool to imagine a heavily augmented street samurai seeing warning pop up in his AR about the errors occurring to his augmentations after getting blasted in the chest with electricity.
On the other hand, I don't feel adding an additional weakness, however minor it may seem at times, it fair or needed. Street Samurai are already weak to hackers with certain gear, they don't need to be weak to magicians with electricity spells or people using stun weapons.
Perhaps it could be hand-waved by the different construction of cybernetics and their fusion with the body. I dunno. Some kind of technobabble.