These files are in /assets/textures:
ion_storm.bmp -- ion "clouds" in Nebulae. Painting it to black will make all ion clouds invisible.
LightFuncHiRes.bmp -- growing groups. Painting it to black will turn off all growing groups.
Polaron-torpedo.bmp -- this file is not used, polaron torpedo uses fx1.bmp for texturing.
skybgnd.bmp -- nebula background.
There are also many bmp files left from SFC:OP not used in SFC3 which can be deleted and will not cause any problem.