If a business sells something at a price that loses them money, the business is not well run. When you ask a shop to order something they should know the cost to them and a price they can sell it at to meet their margins. If you have seen the item you want for less online, tell the shop and ask if they can match it or come closer. If they would lose money trying to match the price then they would be foolish to do so, but they might be able to narrow the gap between their price and the online one to make the sale.

In short, if they are selling things at a price that loses them money, you might as well buy it from them because they won't be around for long anyways.