The damage modifier for small guns doesn't make any sense indeed. A small hand gun inflicts the same kinetic damage regardless of whether I shot a mouse or an elephant; the elephant simply has more mass and can absorb it much better.
This should indeed be handled by the respective damage versus hull values. That'd be more obvious, and in line with any sort of reasonably sensible physics model.
If you from the Start give an Small Weapon 1/3 of the Damage an Large Weapon has. And an Large Ship 3 Times the Hull of an Small Ship. You could Drop such Modifiers alltogether.
But if they did they would also need to Give Large Ships Bigger Shields.
And as I said before. They are trying Hard to give as much Stealth Buffs to Fighters as Possible.
So an System like this where they can Remove 20-30% of an Large Ships Effectiveness without showing it. Is better for them to work with.
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Thicker hull could not be represented with more armor. More armor would affect large weapons against large hulls. Large weapons are unaffected against large hulls. Only smaller weapons are affected against large hulls.
You're being narrow minded. This won't just affect turrets, it will affect all weapons. And you don't bring a bazooka to shoot a motorcycle. Consider that large ships aren't supposed to be great at fighting smaller ones. Actually, large ships already do quite fine against smaller ones.
The elephant has a thicker (harder) skin. The bullet is slowed down some on entry, delivering less than total damage.
To make the example more extreme and more visible, shoot a mouse with a gun and shoot a tank with a small hand gun. The bullet bounces off the tank. The bullet will cleave the mouse in two.
Another extreme example to illustrate the mechanic, throw a dart at a mouse and throw a dart at an elephant. The dart will likely deliver a mortal wound to the mouse. The dart would probably hardly penetrate the elephant's skin.
Maybe you didn't read the post. It's because larger ships have thicker armor. Larger caliber weapons have no issue delivering their damage despite this. Smaller caliber weapons do. So smaller weapons do less damage. It makes perfect sense.
Your Narrow Minded.
If you made such Changes the Weapons Damage would be Revised entirely Anyways.