Shapechange had always been very limited. It turns the subject into a single non-mtahuman non-magical animal of the spellcaster's choice - cyberware and bioware are transformed as well and do not function as such in the new form. It has always been that way.

I feel the same way. Even if cyberware were retained, I don't see the spell re-working all of that nano-implanted micro circuitry so that the golden retriever that you have turned into has functioning cybereyes. Either the spell affects the cyberware, in which case it is changed with everything else when the new form is assumed, or it doesn't, in which case the character is seriously fragged up. Since the former interpretation is more in line with how the spell has always been treated before, it's the one I would use.