I tried downloading your pk3 to take a look but its not working for me.
I noticed that the stormtrooper caps image is missing from that folder as well. In JK2 this link served to cap dismembered body parts, I think that JA may use a shader to cap them. In any case the link may be used by the game engine to run the shader on those areas so leave it in - in any case the filesize reduction will not be much if you remove them. If anyone knows correct me if i'm wrong