It is possible using the hex editor. I believe it is explained in the tutorial, you just have to find the section that deals with that part in the materials section of the m3d. This is actually how glass parts are done in most models. Glass is usually not textured, and is made transparent in the m3d file.
Color and opacity of non textured parts is controlled in by a four byte section that might look like this in your hex editor: 00 FF 00 FF. This describes a pure green part with no transparency. The first three pairs define the color, blue first, then green, then red, and the final pair controls the opacity. 00 is invisible, 35 is a typical glass transparency and ff is of course fully opaque.
So if you can locate the section for your non textured guns you should be able to make them disappear. The only catch may be that more parts than just the guns could be defined in that one section and thus would disappear also.
I hope that helps!