ubiquitin, it is simply not true that most of the chickens are thrown out. The vast majority are processed within 72 hours and then frozen for future use. If it made economic sense to throw them out then that would be the right thing to do, but most of the time it doesn’t make sense, so it doesn’t happen.
You don’t see a fridge at kaporos operations — but neither do you see piles of shechted chickens waiting to be dealt with. The shechted chickens are regularly collected and taken somewhere to be processed.