Hey! I’m using WaniKani Breeze Dark, and I don’t think I’ve had to tweak it in any way. I’m using Stylus rather than Stylish though, but that shouldn’t make any difference in terms of rendering.
There are (pretty simple) instructions how to install it in the linked thread. In case that still doesn’t help, what browser are you using, and what are your settings regarding light/dark mode in the browser and/or globally in the OS?