* Where will topics be stored ? *

On the question of where the list of topics will be stored, the initial thoughts of the Structured Data team would seem to be clear: they are to be stored on the new CommonsData wikibase.

See eg:
https://commons.wikimedia.org/w/index.php?title=File%3AStructured_Data_-_Slides.pdf&page=17  ("topic links")
https://docs.google.com/document/d/1tzwGtXRyK3o2ZEfc85RJ978znRdrf9EkqdJ0zVjmQqs  (API design and class diagram)

* What about the natural hierarchical structure ? *

eg

Leonardo da Vinci
-->  Mona Lisa
-->  -->  Files depicting the Mona Lisa

Shouldn't the fact that it was Leonardo that painted the Mona Lisa only be stored in one place, on Mona Lisa, (or perhaps on Leonardo); but *not* multiple times, separately on every single depiction file?

*A*:  Probably not, for several reasons.