There are pretty sophisticated machines out there for non destructive machine inspections. Many based on X-ray or MRI technology depending on the materials.
Similar to the machines used to inspect shipping containers. I would not be surprised if SpaceX had at least considered if not obtained equipment for the ability to X-ray the entire assembled rocket for any internal defects.
Anyone curious can take a look at the equipment from Yxlon (http://www.yxlon.com) for examples of COTS X-ray based inspection that's available. And Yxlon and most others in this industry do custom work, making a robotic full sized rocket inspection setup, quite a realistic concept when the costs of failure are considered.