That is, it would be counterintuitive if these get cards from my opponent's deck in the battle when cards don't.
I can see also rule that says that these cards just sit there and don't shoot back because there's literally "nobody home" and it's certainly implied that even the computers may be damaged on the two uncontrolled cards that have weapons at all. (These are Starship Defiant and uncontrolled Empok Nor which has "0" weapons, and so could presumably be target of some future card to make them greater than "0"; as it is Defense system upgrade only targets "your facility" and other cards mention "ship.")
Additionally, it would be very odd if the Defiant was able to shoot at multiple attacking ship like a card when it was uncontrolled but then lost that ability when commandeered. It would also be odd to let my opponent pick the targets given that this option was apparently rejected for cards.