Hey I have found a little more info on this issue but at least I hope to point you in the right direction, the confusion seems to be that whisker menu uses GTK 3 these days and so older methods are no longer viable.
Instead, try navigating to '~/.config/gtk-3.0/' and edit (or create) 'gtk.css' in this file you can make changes similar to the older methods, for example:
#whiskermenu-window {
background-color: #404040;
color: #ccc;
}
/* Make sidebar buttons match */
#whiskermenu-window button {
background-color: #404040;
color: #ccc;
}
#whiskermenu-window button:hover {
background-color: #808080;
color: #fff;
}
#whiskermenu-window button:checked {
background-color: #606060;
color: #fff;
}
/* Make treeview match */
#whiskermenu-window treeview {
background-color: #404040;
color: #ccc;
}
#whiskermenu-window treeview:hover {
background-color: #808080;
color: #fff;
}
and then re-login to see if that has any effect.
Source: https://gottcode.wordpress.com/2017/10/21/theming-whisker-menu-redux/