Magento 2 Shipping Rates Show 0 with Multiple Items in Cart

From what I understand your problem reduces to "If there is a wine type product in the cart, don't show the flat rate and when you order only food type products don't show table rate."
Each shipping method model has a method called proccessAdditionalValidation. You need to rewrite the models Mage_Shipping_Model_Carrier_Flatrate and Mage_Shipping_Model_Carrier_Tablerate and implement this method. The method receives as parameter an object of type Mage_Shipping_Model_Rate_Request from which you can access all products.

so your method can look something like this:

public function proccessAdditionalValidation(Mage_Shipping_Model_Rate_Request $request)
{
    //get all cart items
    $items = $request->getAllItems();
    //loop through the items and check their type
    foreach ($items as $item) {
        $product = $item->getProduct();
        //on the table rate model use this
        if ($product is of type wine) { //replace this with your code that checks if product is of type wine
            //so if there is at least one wine product then show the method
            return $this;
        }
        //on the flat rate model use this
        if ($product is of type wine) { //replace this with your code that checks if product is of type wine
            //so if there is at least one wine product then don't show the method
            return false;
        }

    }

}

By default that isn't possible, you must, at least implement:

• A custom Shipping Method
• A custom Shipping Form for your method, to allow customer select different shipping method for each item.
• Create sales_quote_item and sales_order_item attributes to save customer method selection

Your custom shipping method must handle all that logic, you need to split all items/weights and calculate the individual/total shipping cost/price and eventually some combination too ie:

- item 1 by usps = $10.
- item 2 by usps = $10.
- item 1 and 2 by usps = $15

Your shipping method must be able to:

• Obtain the shipping cost/price from the others shipping methods (for each single or combination possible item selection)
• Save customer shipping selection to sales_quote_item
• Recalculate all that data in all further steps in checkout
• Save quote_item data to order_item
• Re-implement any other -parent- shipping method feature, like Api calls for pickup, packages generation or tracking number getters

Finally if you want to give your customers a good communication feedback, you should modify all "post place order" email and templates in order to display all that information.

IMO is a lot of work to do, and I can't figure out a real-life case in which such effort would by justified.

EDIT

I'm not totally sure, but a partial use of some dropship extension may help... I guess