While not that extreme, I've always had problems with flickering black areas on certain parts of ships at certain distances after they take damage This is over multiple patches, a switch to a new vid card, and with and without any number of mods. Try sliding the "3D ship damage" slider all the way to the left under graphics options. For me, that gets rid of the artifacts (but also gets rid of the cool 3D damage). Obviously the problem in my case lies with something in the 3D damage textures and how they are applied to certain ships at certain LODs. The artifacts usually disappear if I view the ship up close.
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-AKD
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