Completely unsubstantiated on my part, but I think that it may have been both for stylistic reasons as well as to make the lighting engine look better / hide certain imperfections. For example, the contrast between well-lit areas and dark ones would be better than if we tried the same lighting effect with bright ambient light everywhere.

Given what I've read about the guys at id though, it's equally plausible that they just liked dark, moody environments and figured their fans would be fine with it. Consider the debate that happened after the initial demos of Diablo 3 came out and some fans were outraged at how "cheerful" the colors were and Blizzard responded with critiques of fan recolorings of demo environments. In the end, they released the Reaper of Souls expansion which had a really dull palette compared to the rest of the world along with responses to other game direction criticisms. Being "tasteful" is not necessary for commercial success in the market today and I suspect it was even less necessary back in the mid-90s.