If it’s just your own little tool and you don’t intend to share it with others: do whatever you want. SQL or NoSQL or JSON, it doesn’t matter. Use your own judgement.
In my experience tho most homegrown JSON-based “databases” tend to load all data into the memory, simply because they are very simplistic (serialize everything into JSON and write to disk, deserialize everything into a struct). If your dataset is too big for that, just go straight for a full-fledged database.