I had similar issue with random icons missing from GTK apps.
Root cause was incorrect setting for option gtk.iconTheme.name. Instead of Adwaita it was set to non-existing Adwaita-dark.
I just found this post after encountering the same issue: missing icons within GTK applications such as Gnome Files, Pavucontrol, and Ghostty after switching to Stylix for theming in NixOS.
I was able to resolve it by changing my gtk icon theme in my home-manager config as follows:
As you can see, I had to disable/comment out the Breeze icons and use Adwaita icons instead. A quick logout or restart later, the icons were back!
Note: I had tried simply installing the Adwaita icon packages in my NixOS system config to make them available, but that still didn’t work, so I had to apply them this way in home-manager to get them back.