Yeah that sure sounds like a pain, but for me it would depend on the price. If it were the cheapest around I would probably deal with the hassle. If it were more expensive then I would go elsewhere.
I'll avoid stores like that if possible. I've tried to buy ammo at Meijers on occasion and find it very frustrating most of the time. You have to hunt high and low for someone to open the cabinet and once they do, if it's the older gentleman, he'll simply hand you what you need but if it's one of the women that work in the area, they'll walk you to the front counter. There's a register right there, but it's never used.
Lately, if I'm buying ammo, I end up just buying when I'm down at Atterbury. They beat everyones prices anyway and usually have much more in stock.
I would explain to the customers why the toolbox policy is in effect. Most reasonable folks will understand a business trying to prevent theft. Maybe they should also install cameras in a prominent position by the ammo so the thieves could see they are on camera.