I think learning with a network aligns with how our brain works better than learning linearly. In this sense, zettelkasten is a superior system than Anki, but I do come to realize that a network is harder to maintain as it's missing a clear starting point. Also I find it harder to recall, especially compared with linear stories.
Another constant problem with any spaced repetition system is that you learn by repeating word by word, but essentially we memorize by adding more edges to the node of knowledge, just like how you know a person better if you add more tag to them: my son's friend/ our neighbor/ the boy who owns the white dog, etc. I'm pretty optimistic about this problem being solved by the next gen SRS: using AI to come up with different frames/description of the same knowledge.
If it's prerequisite relationship, you need to make sure that when A points to B, and B points to C, C doesn't point to A. Otherwise you're creating a loop.