Why does Fish shell have dark blue as the default color for directories
Technically that isn't fish doing the coloring. It's the ls command. However, fish does wrap the command in a ls function which tells the command to color the output and use the colors specified by the dircolors command if it is installed. If you don't want the coloring you can create your own ls function that omits the --color=auto flag. Or you can define your own $LS_COLORS env var to keep from using the colors provided by dircolors.