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In theory, I kinda mapped out the center mass of each ship to apply max force to cause max damage. Take in account for the enemy turning and movements as factors that may vary. I Alway thought the middle of the ship is where the hull is and that can be true as well.
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I believe hitting the enemy ship in a way your velocity vector would go through their centre of mass or not does not make a difference in terms of damage.
We know impact damage (the damage rams, terrain and mines do) is responsible for bouncing ships around, from experimentation with different ammo type and buffed/unbuffed mines we also know higher impact damage means more bouncy.
Now, if the damage was increased by hitting an enemy ship towards its centre of mass it would mean both your and their ship would get pushed away from each other more post ram. Since the ram has different effects on the enemy ship depending where you hit it in relation to its centre of mass, a quality statement about the relation of the damages can only be made by observing the ramming ship. However, in some tests to that I never noticed a huge difference in the ramming ship's behavious after the ram. Small differences could occur by minimal derivations in testing conditions which could not be controled. (It is damn hard to produce the same test over and over in this game)
It can be concluded that either there is no or a insignificant difference in damage depending on where you hit the enemy ship.
@ Wundsalz where the centre of mass of ships is can be estimated by testing with rams. Ram a ship closer to its centre of mass and you shove it more, ram it farer from it and you make it rotate more. Since you can't turn a ship's vertical axle by ramming it, you can assume the centre of mass is actually more like an axle of mass.