@MrMoody - I think you’re out on a very big limb.
It is interesting speculation, but I think there’s more to the missing mass observation about the universe than the superficial similarity with masses missing in atoms.
If your theory were correct, the universe itself could be split to create mind bending atomic explosions.
My understanding from the article is that binding energy is energy that is lost, not energy that is truly invisible or never was there to begin with. Therefore I don't think you can draw a connection between this and the missing mass in the universe, which scientists admit they can't even observe.
I do think you raise an interesting idea, however.