Database
[{"_id":{"$oid":"65fc6b08a0ffe6dd598b114e"},"userId":{"KEY1":["1","2","3"],"KEY2":["A","Z"],"KEY3":[],"KEY4":[]}},{"_id":{"$oid":"22fc6b11a0ff111d598b114f"},"userId":{"KEY1":["4","5","6"],"KEY2":["Z","X"],"KEY3":[],"KEY4":[]}}]
Query
db.collection.aggregate([{$set:{allKEYs:{$objectToArray:"$userId"}}},{$match:{"allKEYs.v":{$in:["2","X"]}}},{$unset:"allKEYs"}])