Pokemon Sun/Moon only seems to support stereoscopic 3D with Poke Finder

Pokemon Sun and Pokemon Moon will have some stereoscopic 3D support, but its usage appears to be very minimal. IGN’s Jose Otero, who went hands-on with the games recently along with other media as part of a press tour, says he was told that the feature only works with Poke Finder.

Pokemon X/Y and Omega Ruby/Alpha Sapphire all included 3D. It was disabled in a majority of the overworld, though the functionality was offered in most battles. The engine struggled at times, so cutting back on stereoscopic 3D should improve Sun/Moon’s performance.

Source