What is the recommended equivalent of cascaded delete in MongoDB for N:M relationships?

What you are doing is the best and most optimal way of doing it in Mongo. I am in a similar situation and after going all possible implementations of the N:M design pattern, have also arrived to this same solution.

Apparently, This is not a mongodb thing, but more of a concept of NoSQL, wherein, the less changing data (Courses) can be kept separately. And since deleting a Course is not going to be a very frequent operation, its feasible enough to go through all the records to remove it.

On the other hand, you could let it be as it is. In your application logic, just ignore the values of Courses in the Student document that don't have a reference_id in the Course document at all. But in that case, you must make sure that old deleted Course_id's are not being reused.

OR just use the deleted flags on the Course document and handle everything else in your application logic.

I'm going to answer based on Mongo team recommendations. I also came from the relational database and I had some issues at the beginning understanding the concepts. Mongo team recommends to design with the idea of "Application-Driven" schema, so you have to figure out first what pieces of data go together. Remember there's not such a transaction concept in any possible way in Mongo, even if we invent a driver that handles transactions we should implement our own solution for this. It means if I have two business objects that requires to be updated at the same time always and I cannot tolerate a failure in this operation, I have to join them into a single document (atomic).

In your case you have two documents, Student and Courses, and a relation between then (A student enrolls to N courses). I assume courses are not required to be altered all the time, so they can be stored in a different collection. But the point is the relation between them, in this case you need to atomically delete a Student and all the courses he enrolled in. So the best suitable solution for this is to embed the relation into Student, and keep a separated Course collection. When you delete the student, the relation is dropped at the same time:

Student Json:

{ _id: ObjectId('...'), name:"John", lastname:"Smith", 
courses: [ 1, 100, 50, 67 ], ...
}

Courses can be a separated collection between them. This is the way to handle it in Mongo. Atomic operations must be embedded into a single document. I assumed Courses is a list of courses that don't change so much, in case they're designed by Student we could change a bit the solution.