For what benefit though?

Much better off storing this in an embedded graph database and use cypher.

MVCC, Indexes, Strong typing, WAL, changefeeds.

The simplicity of markdown and JSON are deceptive. SQLite is a solid choice, but then you deal with graph-relational impedance mismatch.

Simplicity. It’s a bunch of files, trivial to edit, version and develop against. This is important for things sometimes intended to stay relevant for a long time.

I’d flip the question towards the benefits more complicated solutions give you. One conclusion might be “not enough”.