With all of the other themes I have tried, themed apps replace the standard ones. This usually makes it impossible to upgrade the app when new release of that app come out. However, it simply depends on whether the app is upgraded frequently or not.
Example: Launcher Pro and the Android Market are infrequently updated, so it presents no problem for these apps.
Google Maps and Nav, on the other hand, have been getting a lot of updates recently, so those apps could be problematic if themed.
All this being said, I prefer non-themed apps, but there is nothing really systemically wrong with themed apps.
Sent from my Froyo Fascinate using Tapatalk.