The technical reasoning for moving to a database-backed store is twofold, they're running into performance issues with large graphs and, more importantly, want to support live collaboration. There are a wealth of other note applications that are just plaintext and operate fully locally. IMO it's worth the tradeoff, especially if they continue to support exporting to EDN and markdown (which I expect them to). It's not like they're going with something poorly supported, they're using SQLite compiled to WASM.

Doing any sort of structured querying over files sucks bad and performs even worse.