Doesn't just putting the cards in order of concepts essentially accomplish this? When I was doing Anki I adjusted my new card rate so my retention rate stayed above 90%. If you do it this way then your chances of getting stuck in a certain areas of the dependency graph (if you were to model it) is pretty low. If it does end up happening then do some extra study on those concepts outside of SRS. This way you don't have to model the actual dependency graph.

You really shouldn't be doing all your study in SRS anyways because so called "flashcard blindness" (i.e. only being able to recall the concepts in the context of your SRS program) is a real thing.

Furthermore, in my experience, what really made Anki effective for me was to write my new cards just in time. Meaning no pre-made decks except for something like the primitives of what you are studying (i.e. symbol names, alphabets, extreme base level concepts, etc). When you write your cards just in time you can really connect the context of what you are learning to the concept. From this perspective it really seems strange to build an entire ontology based on dependency graphs of a concept you haven't even learned yet!