Had Zeiss chipped the lenses, they would have been able to communicate with some Nikon bodies. This allowed certain bodies to meter with the lenses (since they had no actual physical link to the lenses, and therefore couldn't determine the maximum aperture or focal length of the lenses). The N80 is, I believe, a camera that works this way.
Some bodies (F6 and D200 come to mind) allow the user to enter data about the lens (largest aperture and focal length) into an on-board list, so that the user can tell the camera which lens is mounted. Once that data's been entered, the camera can display the aperture set on the lens in the viewfinder. (I don't know if the electronic rangefinder/focus confirmation light requires the lens data to be entered, but I believe it does.)
Regardless, a significant number of the current Nikon bodies work well with Ai-S lenses. Both of the film bodies that will remain (F6 and FM10) do, as do the D200, D2X, and D2Hs. Only the low-end digital bodies won't meter with the manual lenses.
I'm an old-school, prime lens and manual focus guy, so the Zeiss lenses aren't limited for me. I like the idea of the Zeiss lenses, although the cost will likely be more than I'm willing to pay for now.
As to chipping the lenses...I can understand why some people would want that, just as I can understand why some would have preferred that they come in Canon EOS mount. People around here are expressing their desire that the lenses could have been more useful to them...certainly understandable. But on some other forums I've seen people who have gone far beyond expressing their disappointment...people who are actually furious that Zeiss didn't give them what they wanted. As I said earlier, I'm sure Zeiss has their reasons for their decision, and I hope that it works out for them. My reasons, I admit freely, are completely selfish.
Be well.
Dave