How big is/are your *.tscn file(s)?
A possible reason for long loading times are big scene files which often result from using embedded resources (i.e. textures). And yes, this could be caused by making some resource unique. How big is your *.tscn file?
I would recommend just going the normal way. Which is saving meshes and textures in the projects file system and not in the scene. You can check this by moving the mouse pointer over some texture/mesh and see if the path is inside the scene *.tscn or in an own file.
You can move resources out of a scene just by saving (if it is not already present as file) the resource to a file. Just right click and select save. All equal resources then can simply be loaded from that file (again, right click).
Naturally, there are also reasons for making resources unique. And that is if some definitions are actually changed/different. In case of bigger resources it might be useful to go other ways like i.e. saving a node as a new scene and linking it to the current scene. You can then ovverride individually some settings in linked copies of the scene.