I'm not sure but i think the damage calculated by the ships
armour value. If you notice in CR's it has a list of the weapon damage, shield strength and armour value of each ship/defence.
The structure points have nothing to do with the actual damage calculation, they are simply the total Metal + Crystal it cost to construct the ship and represent what will be added to the combats TD for each destroyed unit.
At armour tech 10 a Battlecruiser has 10000 armour value. (may be wrong but what the hell).
At weapon tech 10 a Destroyer has 4000 weapon damage.
I beleive i read somewhere that each shot gives a percentage chance, depending on the remaining armour value of a ship after the shot, to explode, thus destroying it. Here is my example:
A Destroyer fires upon a Battlecruiser for 4000 damage, 4000 is 40% of 10000. This means that from a single shot by a Destroyer there is a 40% chance that the Battlecruiser will be destroyed and a 60% chance it will survive. I beleive the armour value stays at the reduced value for the remainder of the round then resets to 100% at the end of the round.
This means if the Battlecruiser survives the shot from the Destroyer it is left with 6000 armour value, if it takes
another shot from another Destroyer it's armour value is reduced to 2000, giving it an 80% chance to be destroyed and a 20% chance to survive. This would continue until there is a 100% chance to be destroyed.
This damage and armour value is an example and is obviously affected by the WSA levels, also it doesen't take into account the shield buffer.
I must remind you that this isn't an official statement, i read it somewhere for a similar game and am not sure it applies in ZE. It does however, make quite a lot of sense.
I hope my explanation helped.
-Istalris-