I have a good relationship with the Microsoft team behind Code Push. After speaking with them about this exact topic multiple times, they are sure that not only are JavaScript updates allowed, but they will continue to be allowed, as it is stated in the Apple Developer Agreement [1].

There is also a growing ecosystem of open source projects and companies offering services that offer and facilitate over the air updates.

[1] https://developer.apple.com/programs/ios/information/iOS_Pro...