The question is old, but the problem is still relevant. The Cordova plugin, called the hot code plugin, has recently been released. You can check it out. Using it, you can update all your web content that is packaged in the application: JS, CSS, HTML, images, etc. But if you want to add new plugins to the application, you will have to release a new version in stores.
Unfortunately, now this plugin only supports iOS and Android, but perhaps this will be enough.
About Apple policy: you can update your application in this way, but only if this does not change the original purpose of the application. If the application was released as a calculator, but after the update it becomes a game - Apple may ban you.
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