JSON stringify in Node JS not serializing array of objects
Because Waterline queries return models, not plain javascript objects, they have additional properties and functions on them. One of these is an overridden toJSON() function which removes attributes that have not been populated. What seems to be happening here is that you are attaching objects to a parent model which doesn't know it has children that have been populated so it strips off the values.
The reasoning behind this is so that if you query for all Users and don't populate Rooms you don't get an incorrect result showing an empty rooms array.
I'm not sure what all you are manipulating here but the reason it works if you _.cloneDeep is because it removes the custom toJSON field. This is the recommend strategy when you are mutating a parent object from a query like this.