It doesn't make sense for Nikon to spend millions of dollars to develop their own 36 mp sensor just for a low volume body. Particularly not when they can slip in the 36mp sensor from Sony. All the Camera makers are struggling, and money is tight. I'd give a chief engineer a quick trip to the unemployment line if he suggested something like this without a very good reason (ROI). However, Nikon is doing some strange things and paying for it in slow sales and reduced profits.
Judging by the fact that both of the recent 24mp sensors (D3200 and D5200) are Nikon designs but perform very similarly to Sony's past 16mp chip (D5100, D7000), Sony has probably licensed some part of their ADC tech to Nikon.
Considering that, I don't think that they have to put in too much effort to design a new 36mp, AA filter-free sensor, and designing a new sensor from the ground up to not have an AA filter could lead to new performance heights.
I think there would be a reasonable market for a high-MP pro body, especially if it included high fps in various crop modes, as the D800 has already hinted at (5mp in 1.2x or 1.5x). Something like 6-8 fps in 1.2x and 10fps in 1.5x crop would be very desirable IMO. All that is in addition to packing that sensor into a truly pro-level body, which the D800 just isn't.
Moreover, according to Nikon's quarterly earnings statement, they're selling more cameras and making more profit off of their imaging division than ever before; their precision instruments division (microscopes, etc) is to blame for their recent awful performance. http://nikonrumors.com/2012/08/08/nikon-q1-financial-results-net-profit-fell-by-almost-50.aspx/
A bit off topic, but both companies are in the same boat right now in that they're trying to push FF on the masses and seem to be threatening to limit the choices in crop bodies to this end (as has been discussed ad nauseaum elsewhere on this forum), but haven't released the bodies necessary to make this a reality yet.