Some merchants use the pattern where they give away products but charge a shipping fee for the order based on the products. In that case, they may very well be making a profit off the shipping fee charged. In order to figure out how much money made in these kinds of transactions, I added a feature to Profiteer App for that.
The App lets you set an amount for shipping a freebie or zero-cost product. For example, say you ship an item like that for 7.95. When the App processes the order, instead of recording the Shopify selling price of 0.0, the App will substitute 7.95. If you set your COGS on that product to be 2.00, the App will correctly show your profit as 5.95.