At this time when a ship has infantry or other units stacked on it, the "passenger" units take damage first. In anything close to reality, a passenger, cargo, troops, or equipment, on a ship would not improve the ship's survivability. It would hurt it by slowing it down due to the additional weight. To make this a better simulation the ships should take damage to the ship and its hit points should not be increased by anything other than stacking ships.
Without fixing this error, the simulation is flawed so that a ship could add hundreds of infantry to defeat numerous subs or other ships of greater numbers.