Apple isn't telling all the AppStore developers suddenly "port all your apps to x86 now!" for a very very good reason. If they did however, Google would be jumping up and down in joy: the biggest advantage of Apple gone! No more overwhelming amount of Apps, especially for tablets, compared to Android Market!
You have a misunderstanding of Apple's development tools. Adding a new CPU binary to an existing app for Apple developers is trivial - just a recompile. There would be no significant change in the number of iOS apps for either iPhone of iPad. This is one of the reasons that Apple has been at pains to ensure that iOS developers only use Apple's tool chain. It allows Apple to make significant changes to the underlying platform and/or CPU architecture, and have iOS developers' apps just work with a simple recompile.
The people a switch of iOS to intel it might screw is third parties who have developed tools to create iOS apps. Its not clear that apps created with these third party tools would recompile quite as smoothly for an intel iOS. For Apple this would be seen as a bonus. They'd get to mess with Adobe and others promoting cross-platform mobile development tools AND punish Samsung for what Apple sees as the Galaxy Tab betrayal.