What could be envisioned is a split between classes of cameras and the types of lenses they support natively. We have already seen a move in that direction by the various Dx0-D3xxx - D5xxx - D7xxx models on one hand that have no aperture follower and thus cannot meter with anything without a (native) CPU, and the higher-end cameras D200/D300 plus the single-digit pro-models on the other hand all of which have an aperture follower and thus support metering for lenses without CPU (to some extent).
However, all current Nikons do have an aperture stop-down lever in their mirror box, and that is all what it takes to function with non-E lenses in the future. As long as this stop-down lever is present, all "G" lenses will be supported, and by implication, in fact any lens hosting a CPU capable of communicating with the camera.
Since we already know nearly all manual Nikkors (or lenses with F mount) can be enhanced by installing a CPU in them, there is little to worry about for the future.