The "holes" are just window dressing, and have nothing to do with a ship's damage at all. You might notice on some ships that there will be only 3 holes in its side, even though you had six impacts at six different locations. The "artist" of the holes only put three on the side of the ship though... Same with shell holes. Some ships will have no damage showing, yet sinking faster than a stone... Sinking (generally) is in the hit points, and flooding times of the boxes and spheres on a ship's zon file.
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