And the famous "Qu'est-ce que c'est que cette chose là ?", meaning "what is this thing", but literally "what is this that this is that this thing there?"

I'm a little confused, why is the second "que" there? Why can't it just be "Qu'est-ce que c'est cette chose-là?"? (I'd expect it to be the equivalent of "What is it that it's that thing there?")

It's decorative, it has no meaning.

Similarly you have "les choses que l'on voit" and "les choses qu'on voit" with the "l'" being there for prettyness.

Oh huh, merci!

As a French-3rd-language learner (first English, then a little Spanish) I was (and am still) really confused about why "qu'est-ce que" is a thing. Spanish doesn't do that, at least as far as I recall. In many respects the languages have similar vocabulary (at least, coming from an English-speaking perspective).

You can just say « Qu’est-ce ? » as well which is literally "what is it" ;) (written form rather than colloquial)

You could, and it would be correct. But few would understand at first. It sounds like "caisse", like in "caisse de vin" (crate of wine).

It's much more understandable if you add "donc" after "Qu'est ce". I don't really know why, it just adds extra weirdness :)

Can you say "Quoi est-ce?" and avoid that ambiguity (and correspondingly, "Qui est-ce?")? Or would that be wrong?

"Qui est-ce ?" is correct. "Quoi est-ce ?" is not. "Quand est-ce" and "Où est-ce" work. "Comment est-ce ?" doesn't really work by itself but could work with something after it, like "Comment est ce film ?".

All of these work and sound more natural in spoken language if you flip and say C'est quoi ? C'est qui ? C'est quand ? etc.

You can't, the "liaison" is mandatory between "quoi" and "est".

It could also be used by an "homme de lettre" in a very pompous way.