Local JSON file vs MySql database
The question really depends on what kind of querying of the JSON data you're doing, but I suspect if your data grows large enough (or when your use cases become complex enough) you'll find the file processing operations you're doing with fs-extra will be outperformed by the equivalent operations in a database, such as MySQL, especially because you mentioned the JSON file is accessed remotely since it's stored on the server, rather than the client's end.
I think local JSON files are good on the client's end for simple things like user app settings and user preferences, and fine to store on the server for basic things like the navigation menu's structure of the website, for example. But I wouldn't plan to store the main data of the application in a file, rather you'll likely be better off storing it in a database.