I had a very similar problem on a Windows Embedded 8.1 Handheld device. In order to to enable the bar code scanner replace the current device capability with this.
<DeviceCapability Name="C243FFBD-3AFC-45E9-B3D3-2BA18BC7EBC5"/>
This is actually mentioned in the article on MSDN for how to create a bar code scanner application, which can be found here, but it isn't overly obvious.
After doing that the application should deploy. If you still have problems with it not scanning bar codes then try setting the bar code symbologies for the ClaimedBarcodeScanner after you've claimed it to the bar code types you want it to scan. For example the following enables the GS1 128 bar code symbology:
await claimedScanner.SetActiveSymbologiesAsync(new List<uint> {BarcodeSymbologies.Gs1128});
Everything else you need to know about how to get the data from the bar code scanner can be found in the afore mentioned article.