What exactly is the issue with the shaders? Wanting GLSL over ARB asm or not wanting to use id's shaders? Because a shader is all math and math, I far as I know, can't be copyrighted so you're probably be safe in using them.
Wanting a confirmed GPL system. Whether it is new ARB shaders, or GLSL. Using id's is a grey area, ie no one from a knowledgable legal standing has said yes you can use them and no one likes being in legal grey areas.
If it was OK, then I'd say TTimo would not have initially opened the ticket over at github(and then closed it when there was lots of initial talk of GLSL although none of it was ever completed). Current, existing ARB shaders from your projects and others, unfortunately, have many compatibility issues with many graphics cards. Particularly of the ATI variety.
so at the moment there is no real, stable, compatible solution to a GPL engine based game, regardless if it's ARB or GLSL. Either would work, but none exist.
The Dark Mod's "post process shader" has similar driver problems to those seen with Sikkmod or other Doom 3 mods but those have been overcome in the upcoming release simply by renaming the executable to "TheDarkMod.exe" so that ATI and Nvidia's drivers don't try to "optimize" the ARB code. That said, it would be great if the drivers could optimize the code for their respective hardware vendor and GLSL would make that happen by default in most cases.
I think the main drive for GLSL is so that newer techniques and branching can be added at a later time by amateur programmers on an experimental basis in a similar fashion to all the tinkering done with the ARB shaders for Doom 3. Without the complete set, someone tinkering with a small change can't "release" their work and expect people to try it out.
@Sikkpin: Incidentally, I would love to see what you could do with "just" ARB shaders and access to the renderer (remove the depth buffer hacks). I'm sure it would be magnificent in spite of the GL 2.0 limitations. Plus it would be a cool exercise to see what you could achieve visually with SM 2.0 hardware...
(I'm sure that's a broken record request by now though.