I believe they will make good. It sounds like a clerk messed up. I don't blame you for being upset.
I would call the manager and politely ask if you could get a free case or some ammo for the weapon. You know, "Look, I know this wasn't intentional. But I would like something for my trouble. I was told my gun was in, made a special trip and nothing. And I don't even know when my gun will be in. You can se why I'm a little upset."
You should ask for something. Worst he can say is no. If he does, ask for a refund. "Well, can I get my money back then?" And don't say another word. A good manager will want to make it right. If he doesn't, get the gun and find another shop.
I guess you have figured out that it is always a bad idea to pay in advancel for an item or service you have not yet received.
Back in the early 90s I got a Tok and a Nagant revolver special order (this was when they first started coming into the country.) My guy wouldn't even take a deposit. "Pay for it when they come in. If you don't pick them up, I'll sell them to someone else."
That's how it ought to be.