For my games, I do use Armor-only stats for Enemy Drones as well. When they take Matrix damage, it comes off of the same Armor. I don't think of vehicle Armor as armor plating; I think of it as total functionality of the drone/vehicle. Data Spikes fry the insides, and bullets damage the outsides, but they can both take down a drone.
I use Logic (or the rigger's Logic) for the Matrix defense of the drone. If a rigger wants to, they can buy a Firewall Amp to help protect their drones. You can make anything an Amp in Anarchy, so make a RCC Amp.
Drones can also be repaired with Engineering and be back in the fight next Narration.
Shameless Plug: I have the stats for a lot of rebalanced NPCs, including drones, at
www.surprisethreat.com.