There is no difference in that regard between the original iPad and iPad3
In terms of resolution, if images are optimized for 1024x768, they would not be taking advantage of the iPad 3's screen. using a larger document size would indicate to the designer that things are large enough.
That is, IMO, a tremendous waste of time and effort. Using 144 ppi images on a 1024x768 InDesign document and creating the folio at 2048x1356 will provide excellent quality and allow you to target both devices with one set of files. The only caveat is for overlays that are not resampled. In this case create those on separate layers and turn on only the appropriate one when adding the article.