Diffuse and Glow, while they _can_ possess a transparent channel, rarely if ever, actually need one. Point in fact, I have yet to see a single ship where the diffuse and/or glow had or needed one. Best practice: When in doubt, don't.
Transparent parts like windows are the only cases where a diffuse map should have alpha channel. Cockpit glass usually has it's own texture for this purpose, so it follows that normally the ship textures don't need alpha channel. Glowmaps shouldn't ever need alpha channel since they are, by definition, using additive blending already - black on glowmap equals no glow.
Shinemaps should always have alpha channel, because the environmental mapping needs to be addressed in some way, seeing how FS2_Open uses the alpha envmapping by default these days. Simplest option is to just make the alpha channel full black, which results in zero envmapping intensity.
Shinemap brightness is sort of amount of light reflected. Bright areas shine much, dark areas hardly reflect ?
Not quite. Diffuse map (ie. the basic texture) tells the amount and colour of diffuse
(non-shiny) reflection of light from light sources in the game.
Shinemap (RGB) tells the intensity and colour of specular reflection of light sources.
Light sources mean suns, blobs, beams and such.
Environmental map (alpha channel of shinemaps) tells the intensity of environmental reflections (background reflecting from the model surfaces. Basically starfield, nebulas and planets.) It's basically a grayscale texture withing the shinemap file, separate from the RGB channels that the specular lighting uses.
Continuing on a slight tangent, normal maps affect lighting by telling the game to "tilt" the direction of the surface on pixel-by-pixel basis, which results in different intensity of lighting, which the human eye perceives as geometry changes. Height maps add a parallax effect to parts of the surface that are supposedly on different elevation.
And alpha channel determmixes color/brightness of Shinemap mixed with color brigtness of incoming lightrays ( from nebulae / planets a.s.o )
Not so... the RGB part of shinemap is completely separate from the alpha channel. The alpha channel only addresses the environmental reflection intensity. RGB values alone define the specular lighting. And speak of lightrays in the context of FS2_Open graphics is kinda overestimation AFAIK...
From that, shinemaps should have reduced color depth, vastly increased contrast and clever alpha-channel.
I'll experiment with that, it should help to give textures more "depth"
Not really that simple... <the following is largely based on my preferences, your mileage may vary>
In fact, in my opinion shinemaps (the RGB part anyway) benefit from having an increased saturation compared to the diffuse, but it's largely ship-specific and requires case by case testing. Also, my preference is that shinemaps not be overly bright, but specular intensity settings (cmdline options) tend to have an effect on that as well. What comes to env mapping (alpha channel of shinemaps), in most cases it should be very very close to black. Very dark grey has an useful effect on giving just a hint of environmental reflection to surfaces. Chrome and glass parts should have more intensity, but even then using full alpha brightness is... questionable.
Cockpit glass is interesting case btw. You would think that full white RGB and alpha would give best results, but that's not the case (just take a look at the Tauret to confirm this). Glass actually tends to require medium gray specular (RGB) value and bright environmental (alpha) value.
Also, if the windows have a glow map on them, do not make the glowmap have full intensity. If you do, you might as well drop the windows detail from shinemap, because the glow will drown them out anyway. Reducing the brightness of the glowmap (and possibly increasing the colour saturation slightly) when it comes to windows will give a nice mix of light coming from inside the ship and reflected by specular and environmental reflections. And, of course, the windows should be black in the diffuse map.