I think Dr. Mizuno is dealing with a high standard metalworks shop so they have high rates. Perhaps is not easy for him to find a more economic shop to get the nuts drilled, if that is the problem really. Is hard to imagine what else could be the problem to open it.
As people have stated previously, stainless steel galls easily; it also has a tendency to work harden, making drilling difficult. Some vacuum hardware utilizes silver coated threads to avoid this problem. For example, the threads on VCR fittings are typically plated with silver. I don't know what machining facilities Mizuno has, but if he can get hold of a vertical mill and carbide tooling it should be possible to either drill or mill off the damaged hardware (assuming it is nuts/bolts). I have some experience machining stainless, and the combination of rigid a setup, carbide tooling, and appropriate coolant works well.