[{"id":1,"marcadores":[{"k":"G","v":"00"},{"k":"1","v":"A"},]},{"id":2,"marcadores":[{"k":"1","v":"A"},]},{"id":3,"marcadores":[{"k":"G","v":"03"},{"k":"P","v":"55"}]}]

db.collection.aggregate([{$set:{res:{$filter:{input:"$marcadores",cond:{$and:[{$eq:["$$this.v","00"]},{$eq:["$$this.k","G"]}]}}}}},{$match:{"res.0":{$exists:false}}},{$unset:"res"}])