[{id:1,name:"John Doe",books:[{id:1,title:"The Hobbit",read:false},{id:2,title:"The Lord of the Rings",read:true},{id:3,title:"The Silmarillion",read:false}]},{id:2,name:"Jane Doe",books:[]}]

db.collection.aggregate([{$match:{"id":1}},{$project:{"books":{$filter:{input:"$books",as:"b",cond:{$eq:["$$b.read",false]}}}}}])