Windows Embedded is not a supported OS. There may be ways of getting it to work but this usage is not validated or supported. As far as Media SDK SW fallback is concerned, it should work on all Windows OSs and platforms.
Media SDK is a platform depended hardware acceleration and is provided with OS-specific platform drivers. Please refer to latest MediaSDK release notes on Windows supported OS versions: https://software.intel.com/sites/default/files/mediasdk_release_notes.pdf