I think you will find that this has nothing to do with your app. The scanner is likely connecting in HID mode, so to the iPhone, it looks like a Bluetooth keyboard. IOS will not take up any of the screen with the popup keyboard if it thinks you have a Bluetooth keyboard attached.
Some of our BT scanners support a mode where the user can press a button on the scanner to enable/disable the keyboard on the IOS device. Not sure if the scanner you are using has anything like this.