Next version (With a bit of luck this weekend) will have a lot of fixes and technical improvements in that regard, thank you for reporting.
They purposely ignore them for the moment.
It is not a problem when targetting SCA/FAF, but if you kill "Laser towers" or "Drones" of a real faction, it will lower your reputation, you can easily go from +30 to -30 if during a harass operation you kill 15~20 Laser towers (Some ships haul literally HUNDREDS of them), 10~15 Defence drones (Reasonable amount for any XL ship) and 5 repair drones (Even if they fall to stray fire)... in a single operation!!!
Again, this is not meant to be this way in the future, once I focus on L/XL piracy systems/mechanics this will change, but for the moment, the best option is to put that decision on player hands rather than on AI hands.