[{"_id":"001","a":{"b":{"c":{"custId":"cust1"},"d":{"custId":"cust2"}}}},{"_id":"002","a":{"b":{"c":{"custId":"cust1"},"d":{"custId":"cust3"}}}},{"_id":"003","a":{"b":{"c":{"custId":null},"d":{"custId":"cust2"}}}},{"_id":"004","a":{"b":{"c":{"custId":null},"d":{"custId":"cust1"}}}}]

db.collection.aggregate([{$project:{custIds:{$map:{input:{$objectToArray:"$a.b"},in:"$$this.v.custId"}}}},{$unwind:"$custIds"},{$match:{custIds:{$ne:null}}},{$group:{_id:"$custIds",count:{$sum:1},records:{$addToSet:"$_id"}}}])