It would in the sense that the alteration would be the the universal material file, but it would only actually effect the ship which is drawing on the newly added material.
So assuming that you didn't replace an existing texture file and only added a new one, with the corresponding name to the one applied to the mesh it wouldn't change anything on any of the other Kusari ships. At least to the best of my knowledge.
Gosh, now that I've flexed my new found knowledge of how Freelancer operates all I can say is I much prefer this model to the last, writing aside and am greatly pleased with it.