I am building an application that is using JSON / XML files to persist data. This is why I indicated "outside of SQL" in the title.

I understand one benefit of join tables is it makes querying easier with SQL syntax. Since I am using JSON as my storage, I do not have that benefit.

But are there any other benefits when using a separate join table when expressing a many-to-many relationship? The exact expression I want to express is one entity's dependency on another. I could do this by just having a "dependencies" field, which would be an array of the IDs of the dependencies.

This approach seems simpler to me than a separate table / entity to track the relation. Am I missing something?

Feel free to ask for more context.