The trick is that the shutter isn't doing the work; the flash is. It's possible to make very short flash pulses; I think you can make them even shorter than the 1/50,000 second mentioned in the article. As long as most of the light for the photograph comes from the brief but intense flash, the ability to freeze action depends on the flash speed rather than the shutter speed. You actually need to make sure the shutter speed is slow enough that the shutter is guaranteed to be all the way open when the flash triggers (X-sync speed or slower), or only the area behind the open part of the shutter will be exposed. Controlling things using the flash also guarantees that the multiple cameras used for 3D photography will all be taking their pictures at exactly the same instant.
Also note that the limitation you're talking about only applies to focal plane shutters (i.e. those right in front of the film or sensor). It's also possible to use a central shutter that's located right next to the iris of the lens. Central shutters open and close like the lens aperture, but block the lens completely when they're closed. Like the lens aperture, they block light to all parts of the focal plane more or less equally as they open and close, so they don't induce any of the motion effects that focal plane shutters do. Central shutters have their own problems- it's hard to make them work for very short shutter speeds, and they have limited efficiency when you use them that way because they're only completely open for part of the time- but they do eliminate focal plane shutter artifacts and allow you to flash sync at any available shutter speed.