Clearly, you don't know much about the iOS Dev environment. Under Apple's current development terms, organizations can already set up and deploy to their own privately managed App Distribution systems for their own privately signed devices. This would be no different.

More specifically, Apple does not pay to have their products placed. They do, however, provide the hardware free-of-charge. There is a distinction there, but it's probably too subtle for most people here.

Simple: It is invasive in that it invades your privacy, and ineffective in that it is all about the perception of security as opposed to actual security. All this does is look under your clothes. If someone really wanted to smuggle a weapon aboard, they'd carry it inside a bodily orifice. Until the TSA starts doing full-body X-rays of all passengers, then this check-point security is entirely for show.

...and go download the new version: http://developer.apple.com/iphone/