Apple purposely kept stock low in stores at the beginning to drum up demand and lines and it worked like a charm. They'll no doubt do the same this time.
The store I went to didn't sell out until Monday and it had long, 4+ hour waits all weekend.
So if your theory is correct, there shouldn't have been any lines on Friday, Saturday, or Sunday, since they had plenty of phones, right? But that's not what happened.
The biggest factor was the activation process. They could only process so many people per hour no matter how many phones they had piled up in the back.