I can confirm that iPad 4 does not solve this problem, at least not using the Lightning AV adapter with HDMI.
I'm using both the iPad 2 and the iPad 4 as a test, outputting a 1920x1080 Keynote presentation to two different plasma monitors. Both seem to be displaying at 1024x768 or at least not full-screen.
Both, however, will play back video shot in the iPads at 1920x1080 full screen.
This is, I believe, a Keynote app issue.