The next D700 will probably still have it's own original Nikon sensor. The current D700 doesn't use a Sony sensor. It's the same sensor from the D3. My guess is that they will go with either 16mp or 18mp with slightly better ISO performance and better dynamic range.
Sony sensors debut on Sony cameras first. Well they do now anyway. Before Sony bought Minolta and started their own DSLR line. Before that they were in Nikon bodies first. If the D90 replacement gets it's own original Nikon sensor (doubt it) then it'll be a huge turning point between Nikon and Sony's partnership.
I'm really fascinated to see Nikon's next move - will they break the 12mp/24mp pattern with a new sensor? If so, won't it be a little weird for them to sell a D90 replacement with a higher mp sensor than the D300s?
Not really. It would explain why the D300S is so heavily discounted along with the D90. Nikon needs to sell as many as they can now before a higher spec and lower cost camera comes out in the new "D90".