Hi,
You can move product B and product A in two different warehouses (that you can configure in the System>Warehouse menu.
Then, you configure you two shipping methods for the warehouse of the product A and you create a free shipping method for the warehouse of product B. That way, the products will be grouped based on their warehouse and each group will have its own shipping methods selection on the checkout.
More simply, you could just set a weight of 0 for that product B and a weight for product A and turn off the "include virtual product prices" setting in your shipping methods so that the price restrictions will ignore product B.
If you want to not do that and use a plugin instead, you could create a new shipping plugin based on the manual shipping plugin and add in it a trigger onShippingDisplay which would be based on the onShippingDisplay function in administrator/components/com_hikashop/helpers/helper.php where you would change the conditions on the prices.