Well, here's something interesting. I found the most obvious mipmapping setting on my card and changed it and then went back to the same scenario I saw the artifacts in above and it seemed gone...until I was messing around later and fired my deck gun at the ship and hit her once. All of sudden the flashing black areas were back along the whole length of the ship. Went to graphics options and slid the "3D damage" slider all the way to the left. The flashing areas went away again.
So, any damage seems to cause this to appear. However, even with the slider all the way to the left, certain areas of ships still exhibit these artifacts until you zoom all the way in (when viewing them in the museum). One of the most obvious areas is elevators on carriers, e.g. Bogue class fore and aft elevator:
The life rafts hanging vertically along the sides of ships are also prime suspects, albeit in a much smaller form.