In addition, defense is much more effective when you have fewer decks (500 defense with 250 decks will be harder to hit the damage cap on as opposed to 500 defense with 1500 decks). So if he has a small number of decks, his "small" amount of defense may be proportionally greater than your attack.

small damage cap, and a large crew size.

low decks high number of crews...Where do all the crew members hang out in a small build ships

What?
Damage per shot = tanh( attack*(random(0.6 to 1.666)) / (defense * 5) ) * damagecap

Defence is just as effective no matter how many decks they have... just the damage goes down because the cap goes down.

Use a Spy Probe-Defenses and a Spy Probe-Weapons to find out his true attack and defense. Also look at his medals and you will be able to see how many decks he currently has (if he is under colossal galaxy destroyer), divide this number by 2 and that will be the max damage that you can do to him.

Best part about hitting a small ship build is that if you are hitting the cap, you can determine exactly how much hull the enemy has. You can sort of do it to larger ships, but you have to track the numbers closer. Small ship cap makes the math tons easier.