If I ask, it is because into Blender, and to save system resources, we can instance objects. So it is with Godot which can instance scenes too. So into the game engine, we could totally duplicate an object and use it as a collision shape, right?
Yes, kinda. You can have a MeshInstance generate a collision shape though by using the mesh button and selecting between a Convex or Trimesh collision shape.
If yes, how Godot is managing this knowing that any addition of mesh will surely have an impact on system resources ?
I have no idea for sure on how the internal structure works, but here's how I think instances/copies are handled in Godot:
Every resource (nodes, meshes, pictures, etc) all have a unique RID (Resource IDentification) number. When a scene is instanced/opened, Godot loads all of the resources and stores them by their RID in a data object like a dictionary. This makes it where Godot does not have to load each resource every time one is instanced.
For example: if you have a cube, it will only load the data for the eight vertices, six faces, and whatever material once and store that data into the proper RID space in the dictionary. Every time that cube is instanced/spawn/created, Godot will take a copy of the mesh data from the dictionary at the cube's RID, instead of loading, parsing, and storing the data all over again.
By storing the RID's, Godot can reduce resource loading time.
There is at least one performance benefit though, because instead of having to go through each node and process using it's resources, Godot can instead go through each node, get the RID's for each resource, and do the processing there.
This makes things a tad faster performance wise because there is less data being tossed around in the code base, since all of the resources are accessible through the RID data storage. Whether or not this helps performance I do not know. I would assume it speeds things up a little bit, especially if you have scenes with lots of data intensive resources.
Now for multi meshes and GPU instancing, this is a completely different topic. Passing data from the CPU to the GPU is slow, so any optimizations in data store provides benefits to performance in those cases.
To summarize: The performance is almost certainly better than if there was no instancing, but the impact on most systems (rendering, physics, etc) will stay the same regardless of instancing or not. Regardless of the performance benefits, I'd recommend instancing because it's easier to manage (over having everything all tossed in one scene)
Another question would be : Can Better Collada Godot plugin export collision meshes coming from Blender ?
Yes. As @MagicLord said, you can use the -col keyword to convert a mesh to a collision mesh when it's imported. The documentation has some of the import hints you can use in Blender.