The decision to not render icons using nautilus anymore, and instead use Gnome shell to render them was an awful decision.
The Gnome shell desktop extension is not as robust as nautilus. If you move a file by dragging and dropping a file, there is a good chance that Gnome shell will hang. I disabled the desktop icons extension because of this.
In principle it was the right decision. Opening an application shouldn't take over the root window. The was specially obvious for people who don't use gnome but use nautilus. The problem is that as you mention "The Gnome shell desktop extension is not as robust as nautilus"
The Gnome shell desktop extension is not as robust as nautilus. If you move a file by dragging and dropping a file, there is a good chance that Gnome shell will hang. I disabled the desktop icons extension because of this.