A higher res D3 version is conjecture of course. But it's informed conjecture.
Firstly, I have heard about it from two well connected industry sources. This is not my brotherinlaw knows someone's second cousin, but rather people whose creditability is well known to me.
Secondly, it's a no-brainer. Just as Canon uses the same body for the 1D MKIII and the 1Ds MKIII, changing essentially only the chip, the same will be true of Nikon with the D3. Anyone that assumes that the D3 at 12MP is what Nikon is going to hang its hat on against Canon's 21MP camera, just isn't thinking.
Timing is everything, of course. The sooner the better in terms of the competitive marketplace. PMA is just a few months away, and then Photokina in the fall, of course, but that seems too far off.
My guess is that Nikon wants to get the D3 rolling, and work out production kinks. I have no idea what yields are like for Sony on a higher-res FF chip, but I'm sure that's a factor as well. It takes time to get yields up and prices down on big pieces of silicon like this.