I hadn't noticed this until now but as I re-engaged a pirate fleet after some ships retreated, I noticed that the damaged armor cells were scattered randomly across the ships, so they all had a "checkerboard" pattern of damage.
My suggestion is to change where the damage is applied. I'd love to see the ships have damage applied across only two or three points (angles from the center) to simulate battle damage (perhaps usually to the rear, since they were retreating?)
It would add to the game immersion (when I re-engage, i notice that there's a large gaping hole in their starboard armor.. hmm my fleet must have gotten some good hits in on this one as it fled.) In addition, it would bring a degree of tactical decision making to the next fight while not making the enemy uniformly weakened (target the starboard side to take it down quicker, but now they can cover with their shield at the risk of opening up the armored port side.)