According to the first comment at the end of this article: http://www.imore.com/keynote-iphone-ipad-review
And here: http://help.apple.com/keynote/ipad/2.2/#/tand1a4ee7c
It seems that you can configure keynote for iPad, such that you can see speaker notes on the iPad when you're using a dongle to plug into a projector or big screen; but not on the big screen.
Is this functionality only afforded to Keynote through some private API in the OS level? or does anyone know of a way of achieving this programatically? My use case doesn't need to make it into the app store - so a private API hack could work for me.
No need for private API's. You can observe UIScreenDidConnectNotification notifications for when a second screen is connected whether it's airplay or hdmi.
You then provide a View/ViewController for that screen.