Sorry, I misunderstood what you were trying to do.
I don’t have enough information in regard to your use cases and hardware, so it’s kind of hard for me to make assumptions related to performances. You should write some tests and see for yourself.
That said, if you store the collection of elements using GridFS you have to read and write (and serialize) all the entries each time you want to access or modify the collection.
So, I’m incline to say that an association will perform better even if you have to store the elements in different documents.