For a long time I didn't use folders to organize my notes. I somehow bought that your notes should be an associative knowledge base that is linked together. I also somehow bought that tag based content addressing is good, even though I never used it really.
These believes I had are quite strange. Using directories neither prevents me from using roam style links nor org tags. Nor do any of these prevent recursive grepping or semantic-embedding-and-search.
All these compose together. And each solves a different problem.
I made a choice where there wasn't any to make. It's like trying to choose between eating only pasta or only kale.
Roam-link links from content to content.
Directories form a sort of decision tree that you can use to iteratively narrow down what content you want to look at, without already having some content at hand.
Semantic search finds possibly related things, when there isn't explicit linking structure. It's implicit ad-hoc generation of linking structure.
One use of tags is to classify what type of thing something is. E.g. :cs:complexity_theory:chaitin: might be a good tag-set, but a terrible directory structure.
Recursive grepping is good old full text search, which can trivially be configured to start from a particular directory root.