A thread with similar question and my answer/opinion: IBM Worklight: Upload application to Worklight Server / App Store
If you're upping the application version and submit the application to the App Store, the update process is similar to that of any other app on the App Store (remember, a Worklight Hybrid application is still contained inside a "native shell").
The end result is that users of v1.0, will receive an update notice for v2.0 of the same app and the app will simply be updated.