Resources are passed by reference (as any object in Godot).
When you "duplicate" an object (a node for example), all properties are copied to the new instance, but resources are "shared" between those two instances, so, if you modify the resource from Object A, you'll see the same changes on the resource of Object B, because they share the same resource.
Make unique ensures that the selected resource is unique, this means that is not longer shared with the other instances and modifying it will not affect the other objects.