On Ubuntu, I would run the following command sudo ln -s /path/to/application.desktop ~/Desktop
And it would copy the .desktop file to the Desktop folder, which would make them display on my actual desktop. It would look like this, for example:
Desktop files and folders are not part of the Gnome DE in the sense that they can be displayed on your visible desktop. Regardless of what lies in your $HOME/Desktop folder.
Instead, Gnome uses what they call Dash.