While you can argue they are still flawed, they do clearly show that the electrons have fairly large probabilities of being observed pretty much anywhere inside the "radius" of the atom.
At this point, arguing about "are atoms mostly empty space" becomes a futile semantic argument. The model you picked in order to defend this statement is indeed useful in some limits, but it has been proven wrong. Imagining electrons as clouds has proven to be much closer to reality.
I have to concede, though, that "empty" is not a particularly meaningful physical concept, quite the opposite. Disregarding the Aether theory, only to replace it with fields of potentials, that is kind of running in circles.
A model is fundamentally wrong. That's what it means to have a model. At that "clouds" is no more helpful then "empty". The fact of the matter is that no one has ever seen these things, no nucleus, no electrons, as far as I know.
Yet, you haven't pointed out what was actually wrong with "Those are simply the electron orbitals which describe the probability of finding the respective election at a given point".
Edit: Perhaps you intended to imply that this description is overly idealized (not to say simple).
If you have too much external pressure (gravity), those smeared electron clouds come too close to the nucleus, react with it, and the only thing left is neutrons.