As far as abstractions go, they are hierarchical. Actually, abstraction is all about breaking up and managing complexity into separate parts, and one would do pretty poorly without any hierarchy in their code.

Even Kodu is hierarchical to a limited degree since each bot is programmed separately, but its not unlimited as in the other examples listed (which I would argue, is necessary to be considered hierarchical).

OP's premise wasn't that "hierarchy exists", but that it's "the correct organization of data." Now you are just glibly pointing out that everything can be structured as a hierarchy. That does not make the case.

I'm not pointing out that everything can be structured in a hierarchy, I'm pointing out that everything needs to be structured in a hierarchy at some point to deal with complexity; these are very different observations.