Mongo Playground

Configuration

[{_id:1,"isComplete":true,questions:[{isDeleted:true},{isDeleted:true}]},{_id:2,"isComplete":true,questions:[{isDeleted:false},{isDeleted:true}]},{_id:3,"isComplete":true,questions:[{isDeleted:true},{}]},]

Query

db.collection.find({isComplete:true,$expr:{$eq:[{$reduce:{input:"$questions",initialValue:0,in:{$sum:["$$value",{$cond:[{$ne:["$$this.isDeleted",true]},1,0]}]}}},0]}})

Result