Capship armor reduces the cardo capacity by 300 units.
It is your choice whether to mount it or not.
Lets say you have a train, you can Wither have it at regular hull / 5000 cap
or armor upgrade 4700 cap.
Isnt it the same as what you are asking for.
Its like you are buying a ship with the expansion on it. by installing aromor, your expansion goes away.
Hope that makes sense. Frankly 5000 capacity is already too much if you ask me. I'd say restrict the traders to 340 cruise speed if they buy the upgrade, now there is a fun aspect.