I bet this is the same in most games and many many "cheaters" just aren't.
Using a black skin that's part of the game is not cheating if you ask me. Editing a skin to have a bright pink that didn't exist in the game however is cheating.
Having played q3 back when myself it was standard though to make _all_ skins be the standard blue skin. The one that came with the game itself originally. That could be considered not cheating and being an anti-cheating technique. I'd say it's something that depends on the game though. Q3 wasn't really about shadows and using your surroundings in that sense because it wasn't set up for realism. You also played with gamma pretty high etc.
Something like Counterstrike or say Ghost Recon however I would very definitely find it cheating if you changed all skins to be the same because of the realism involved. Choosing the right outfit for a map would be part of the game.
This must’ve been early on in q3’s life, ‘keel/fb’ (bright green Keel) has been the preferred enemymodel for quite some time since it’s highly visible, has loud movement sounds, and fills out the hit box pretty well. I always assume my opponent forces fullbright Keel for my model too.
The entirely black skin was 3rd-party content, not an artifact from the official game. But yeah, no big deal either way.
My favorite "cheat" (I prefer hack) was to counter another pathetic cheat in Q1: players using an all-black skin. They would hide in the shadows and get you with a rocket when your back was turned. So I edited my local copy of the skin to be bright pink and made a point of chasing them down at every encounter (lingering in the shadows or not).