On a second reflection I may have oversimplified your point.

There's this trade off between having logically structured databases and having data stores that are faster to access. An all-too-superficial scan saw your point as just an iteration of that, which it may not be.

The word "graph" itself might have a different meaning than in mathematics. Of course something like wikidata is a directed multigraph (or a tuple of incidence relations on the same nodes). Still I was under the impression that you were talking about optimizing data stores for access at the cost of having to explicitly maintain consistence in your code and not be able to rely on the database properties themselves -- like what happens when you move from SQL to Mongo.