Nautilus is a libadwaita apps and those do not support theming, see Why and how libadwaita prevents theming? - #31 by bragefuglseth - Desktop - GNOME Discourse
If you want Nautilus to use a dark color scheme, you can change the color-scheme key in org.gnome.desktop.interface GSettings schema to 'prefer-dark'.
If you do not care about “voiding the warranty”, then there is the option of using the third-party Gradience app to customize Adwaita, which modifies ~/.config/gtk-4.0/gtk.css. And there is also the GTK_THEME environment variable that can force change the theme but that is meant for debugging.