It's not so strange, really. MMF does it.
Yeah, but if MMF does it, it doesn't mean Construct should do it. Why an object should be placed in a layout, when user doesn't want to place it in a layout?
It has to exist somewhere. If you don't want it there when the level starts, just check "Destroy on Startup."
There are non-layout objects too, which don't get placed in the layout. I think that if there's an object type you want to later use in your layout, there shouldn't be need to have an instance of it. There is no such a need even in programming languages - object classes and object types are totally separate.
Also, if you delete the last instance of an object, the object type disappears too. I think that object types should be like Plato's ideas, they should exist in their "own world", in some kind of object bank, and then you could make instances of them in layouts.