I am missing a bit practical experience here because a) I haven't coded a VR app yet (just some experiments in godot 2 with double viewports and gyroscope) and b) I haven't done much in godot 3 yet but...:
In a VR app the GUI - if any- should be an object in 3D space. So you can basically map the GUI to a 2D texture, on a plane or one side of a box etc.
Here are examples for viewports:
https://github.com/godotengine/godot-demo-projects/tree/master/viewport
From the description I guess that "gui_in_3d" is the correct demo.
The second question might be how to interact with the gui. I can imagine that you can use a raycast to determine where the axis of your view hits the 2d plane.
Better for VR might be building the GUI completely in 3D.