For a few weeks now I have been using Nikon D7100, which lacks AA filter just like the D800. So far I have not ran into any banding/moire issues, and the extra pixel sharpness nicely helps Photoscan do its thing.
With D800E and it's sharp 36mpix, keep in mind that unless you use top shelf lens and shoot in optimal conditions (fast shutter, lens sweet spot aperture), most likely you will not see any benefits of using D800E over D800 (or cheaper 24mpix cams for that matter).
Cheers,
Andrew