For ngDesktop the application just uses the icons supplied by the installer, and for ngWeb I simply replaced the files "favicon.ico", "favicon32x32.png" and "favicon192x192.png" in the folder "/application_server/server/webapps/ROOT" of my Dev-Environment, that way the files get deployed to the customers installation.
That way I don't forget to copy the files to the root-directory of the installation of new self-hosting customers.