I think it makes "sense". Nikon is simply following a strategy where megapixel count is not a price differentiation feature.
The D4 has a lower pixel count than the D800 or D600. Same deal.
It actually makes more sense to make a D400 with only 16 mpx because that is more doable from a bandwidth perspective, and is probably why the D4 only has 16 mpx.
The question then becomes if the market will accept an ~$1800 16mpx DX camera when a 24mpx camera can be had for $600. It works in FX land but I'm not sure it would fly in DX land and I think that is a critical part of the overall problem.