There was an issue with connecting iOS devices before the AppBuilder 3.5.0 release. Since then, devices are successfully connected and you can run your app on them using USB cable.
If the devices still don't show on your side, can you confirm if you can see them in iTunes? Also, what desktop operating system and AppBuilder client are you using?
In the meantime, you can deploy your apps on your devices without cable connection: Run Apps Over the Air
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