There seems to be something pretty major missing here, I would assume someone is doing something as trivial as this when it comes to querying and mutating resources that only belongs to the user requesting. At the moment I can only do so when getting a list of the resources. I would like to be able to fetch and update a single record with relationships in the where arguments.

Have you tried

ctx.db.shops({ where: { users_every: { id } } })