Sorry, but it is no accidental coincidence that Apple released a Java update that officially deprecated Java, and then proceeded to announce an App Store at the same time which would not allow deprecated APIs specifically naming Java.
One does not need to proceed from the other.
1. Apple didn't want to continue maintaining their own JVM.
2. Considering Apple will no longer control the JVM, Apple doesn't want to sell products in the Mac App Store that will rely on third party runtimes that may break in the future.
Also, Apple may simply want only native Cocoa apps in the Mac App Store, for a cohesive experience like on iOS. It would not be necessary to deprecate the JVM to do this.