Zero shutter lag is going to be a combination of hardware and software. And from the videos I've seen, there's no lag between shots either, so I'm not sure what you're referring to there.
Overall though, I agree. They should have bumped it to 8MP just to match in a comparison matrix. I've gotta assume there's a reason they went this way, as the HTC Rezound is advertising zero shutter lag too, and it has an 8MP camera.
IIRC, the Source had an early version of the nexus that had an 8mp camera. Given all the speculation, I wouldn't be surprised if I misremember this though, so no promises. Assuming my memory is correct there would be a reason why they went with the 5mp vs the 8mp. I would like to think that they have enough smart people to understand the marketing between the 5 and the 8mp cameras.