Sorry - I had intended to say something about how its done, but then "spaced it" and didn't. Jolyon is correct. It's a radiation treatment that's used. And some of the fakes can be detected as he suggests - especially if only the terminations are smoked. Unfortunately, they can - and do - "cook" the crystals long enough for the disruption to work throughout the entire crystal. Then they are smoked all the way through - like natural smoky quartz can be.
Also unfortunately, natural smoky quartz isn't always completely smoky. Sometimes the "smoke" is wispy, or only seen in part of a crystal. And they can also be found at the other end of the spectrum - jet black throughout. (I have some of those, and know they're natural becuase they were collected at a site that has them by a friend. They litterally came out of his pack in my basement the same day, when we cleaned up his "loot" in my mud sink.)
What I would like to hear from someone clicking in here is whether or not naturally smoky crystals are found in the Hot Springs/Mt. Ida area. I've never been quite sure that they aren't - that a few haven't been found over the years. Knowing this - one way or the other - might help with determining fakes, especially if none have ever been found. All I know is that everyone I personally know who has ever collected in that area has never found any that are smoked.
The difficulty of detecting fakes in some cases - such as this - is what makes the trustworthiness of the source so important.