deep structures are fully supported. (I don't know whether they work
for playbooks or roles - I've never tried them there - but they
definitely work for plugins and modules, and I'm not aware of any plans
to change that.)
The reason we removed that structure for community.general and
community.network was that the structure there was never intended to be
seen by users. It was only used to structure the content of the
collection (c.g has 568 modules) so modules covering similar topics are
in the same directory, making development of the collection easier.
Since it was no longer possible to hide this from users, we decided to
remove the structure.