When you try to use macdeployqt it's work fine and you can see the Frameworks folder in application bundle. But when you try to deploy it using the Apple tools to prepare app and then send to Apple Store you can get errors with 'codesign' tool for frameworks. To fix it you need to copy all Info.plist files from Qt frameworks to Frameworks in your application bundle.
I've attached the script's template which helped me to deploy my application. I hope this help to you!
In this script's template you need to change:
1. <Qt_path> - The path to Qt folder.
2. <app_name> - The path and name of Application bundle without ".app"
3. Team ID - The Mac Developer ID. To get it you need to be a Mac Developer.