Actually you're wrong on the technology, the engine 3DDGH uses (Bishamon) is not only hugely scalable but it's already been adapted to 3DS as a commercial middleware solution. Now obviously some things would take a hit, but as Capcom has shown with their MT Framework Mobile projects on 3DS, you can still manage HDR, self shadowing, 2xAA, depth of field, motion blur, etc, while even using scaled HD assets on 3DS. Silicon Studio most certainly wouldn't be starting from scratch here, hell they helped develop the actual tools for the 3DS GPU, they should probably get even better results than Capcom given their intimate familiarity with the system. Bravely Default looks shockingly good for what it is.
Anyway, platform selection depends mostly on what market From wants to push. If they want the franchise to become viable in Japan then 3DS is the only real option at the moment. If they want to go further in the west then HD consoles are the best bet going forward. In either case Vita doesn't really have good prospects since it's currently bombing hard everywhere and the future's looking grim.
And again, I'd say making a game targeted at the Zelda fanbase available on the same platforms as the Zelda fanbase makes some sense. Wii U would come in ahead of Vita based just off that I think.