GoodReader, IMO the best PDF app for the iPad, got a new update today. There's no new features or interfaces changes, but the according to the changelog the app is now compatible with iOS7.
The developers also said that a "full-scale major update with a new design is coming soon", but there is no timeline on that update.
GoodReader is only the latest iOS app to be receive a compatibility update for iOS7; Amazon released an update for the Kindle app last week and there have been other updates that have gone unreported.
I have seen numerous apps mention compatibility issues in their latest updates, and at this point I am growing increasingly concerned. Just to be safe, I would suggest that everyone update your apps before installing the iOS7 update.
I don't normally bother to keep my apps up to date, but this time I will make an exception.