Nah, the third version won't be FOR the 3DS. I suspect it may have 3DS-enhancements, however. (Heck, look at the encounter graphics on the Fighting trio, it looks like it was MADE for 3D.) Third-versions have never been specifically for another system. (Gold and Silver were Gameboy Colour games that could run on pre-Colour Gameboys, not Gameboy games, so Crystal is no exception.)
Hmm... The Shadow Triad being the Striaton Gym Leaders makes perfect sense, especially since they attempt (and fail) to come up with a reason for being Gym Leaders, which no true Gym Leader would likely be obliged to specify. (Of course, a few, mostly new Gym Leaders like Falkner, Flannery and Janine, give one anyway, but because they want to... Well, Flannery kinda gave it away due to nerves, but meh.)