I wonder if this is "The Masters" collected in Ursula Le Guin's The Wind's Twelve Quarters?
There are no "dark numbers", but there are "black numbers" (i.e. numbers represented using Arabic numerals) and zero is explicitly one of them. The society they live in uses numbers of course, but they are Roman numerals, and are hobbled by a lack of zero, negative numbers, very large numbers, etc.
The dystopian nature of the setting is a post-apocalyptic anti-enlightenment agrarian non-industrial society.
The primary characters are a Kabbalistic group of quite illegal engineers and mathematicians rediscovering measurement, algebra, etc. The society they live in uses numbers of course, but they are Roman numerals, and are hobbled by a lack of zero, negative numbers, very large numbers, etc.
Le Guin remarked in a brief comment preceding the story in the anthology that "The Masters" had been her first actual science fiction story.