Instead of having vertical armor, simply add a "Bombing Run" Button. I don't think ANY old players will have the time to update ALL their ships, so keep it simple with how the game is right now, and simply tell the bombers to do a bombing Run.
How this could work is simple. Once the button has been clicked, the bomber will enter a state where the ship instantly homes in on the target. If not shot down (or its bomb bay is destroyed), the bomber will enter an animation where you see tiny explosions on the ship's surface (Just imagine Explosive Charge's explosion radius cut in half. This would be an aesthetic choice). During the animation, the payload is dropped and the effect occurs.