For gun stores there are two types. Those that have inventory and lots of guns on hand, Like Security Equipment and Young Guns, which is nice to see and you can walk out with what you want, however it's expensive for businesses to keep inventory. Then there's places with little or no inventory, like HI On Target and Danger Close Tactical, which special order things for you. Usually cheaper for the customer and for the business.
I can see why businesses, like the later, need to charge up front because the business will order, pay for, and receive the item. Then a lot of customers will then change their mind and not want the item. Probably the majority would do this if no prepayment is made. The business is stuck with the item and has trouble selling it, even for high in demand items.