Regarding damage causing a ship to become unbalanced, I wonder how hard it would be to change thruster output via the universal tool or YOLOL to re-balance the ship.
Obviously this would make the ship slightly slower over all, and would not be practical during a fight, but if you can do this, then presumably you could also do this to balance asymmetrical ships.
This does mean an asymmetrical ship balanced this way would never be the fastest or most efficient ship, but if you're building an asymmetrical ship, efficiency probably isn't your top priority anyway.