[TomTom]

You can test the .pk3 files with winzip or winrar (just associate .pk3 files with whichever you prefer). You can unzip the shader file too (it is text) and look inside for...
/scripts/gfx_misc.shader

gfx/misc/reticlesimple
{
    nomipmaps
    nopicmip
    {
        map gfx/misc/reticle_eq.tga
        blendfunc filter
    }
}

BTW if you use /sv_pure 0 (unpure server) check also to see if you have a /script subdirectory(s) that might have a bad .shader file (you can test for this by setting /sv_pure 1, exit and restart fritzbot).

It is possible that some mod could modify pak0.pk3 but most mods won't. Generally they will install some of their own pk3 files that may contain a modified version of the files needed. ET will then load the newer version of the file either from the mods own subdirectory (for major mods) or if placed in /etmain then it is used because the packed file is loaded after pak0.pk3 (thus the z prefixing the sniper mod pak files mentioned earlier).

And while the shader and graphic are the most likely corrupted it is also possible that an unrelated file loaded before these is the culprit.
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Using Windows explorer , the way I generally go about finding a problem file in etmain is I create a temp sub-directory, then move all the .pk3 files (except pak0 to pak3) into the temp directory. Then I test one of the 6 official maps and if the problem is gone I move a big chunk of pk3 files back in (no more than half of those that are in the temp directory), then retest, and repeat the move back until I find a group of files where the problem lies. Then I move that bad group into another temp directory and move half of them back, retest etc. eventually finding which file is incompatible. If the original problem only occurs with a particular map ( say a bad map texture) then I leave that map's pk3 file in etmain along with pak0-3 and use it for testing instead of one of the original maps. Basically I do a binary search method.

BTW I tested what the effect of a missing shader etc. would be, And you would not see black, so it is more likely a corruption or conflict.