How can I push a value to a specific array index using mongoose in nodejs?

Would have been a little bit helpful if you had shown your Freezer model schema. Nonetheless the following example is based on the sample data (example):

{
    "_id" : ObjectId("565236570f7f257d5feffa10"),
    "shelves" : [ 
        {
            "racks" : [],
            "shelfname" : "Shelf 1"
        }, 
        {
            "racks" : [],
            "shelfname" : "Shelf 2"
        }, 
        {
            "racks" : [],
            "shelfname" : "Shelf 3"
        }
    ]
}

So, pushing rack data to "Shelf 1" shelf in mongo shell would use the positional $ operator which only supports one level deep and only the first matching element in its update. Note, the shelves array field must appear as part of the query document, hence { "shelves.shelfname": "Shelf 1" }:

db.freezer.update(
    { "shelves.shelfname": "Shelf 1" },
    {
        "$push": {
            "shelves.$.racks": {
                "rackname": 1, 
                "columns": 3, 
                "rows": 2, 
                "spaces" : []       
            }
        }
    }
);

Now, if you knew the specific array index then create the update document using the bracket notation:

var update = { "$push": {} },
    condition = { };

condition["shelves.shelfname"] = "Shelf "+ shelfindex + 1;
update["$push"]["shelves."+ shelfindex +".racks" ] = {
    "rackname": rackname, 
    "columns": columns, 
    "rows": rows, 
    "spaces" : []
};

db.freezer.update(condition, update);

In your node.js, this would be similar but with a callback:

Freezer.update(conditions, update, function (err, doc){
    console.log(doc);
});