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.
I’d flip the question towards the benefits more complicated solutions give you. One conclusion might be “not enough”.
Many single file graph databases out there. They should be "simpler" since it's one file vs many.
Text files vs binary is what you're arguing. Why don't you store your phone address book as a text file?
Everyone know the answer to that one. SQLite is a solid, well accepted answer. You already have 20 of them on your phone.
We need to build a similar option for graphs instead of the markdown detour.