We do not use the UDID in Mendix applications. If your app uses the UDID through the PhoneGap API you will have to update your app use alternatives.
The size of iPhone 5 screen is no problem for Mendix applications either because web applications scale nicely.
The images you use in your app might not be 'retina' but I do not think their policy requires you to have double resolution images everywhere. Text automatically gets rendered sharply.