No mongo 3.2, o código a seguir parece funcionar
db.collectionb.aggregate([
{
$lookup:
{
from: "collectiona",
localField: "collectionb_fk",
foreignField: "collectiona_fk",
as: "matched_docs"
}
},
{
$match: { "matched_docs": { $eq: [] } }
}
]);
com base neste exemplo https://docs.mongodb.com/manual/reference/operator/aggregation/lookup/#use-lookup-with-an-array