Do you have an original model 3DS or 3DS XL? Well according to Nintendolife these older handhelds won't support Hyrule Warriors Legends in stereoscopic 3D. Apparently the hardware just isn't strong enough to maintain the game at a steady framerate--a game which has dozens of enemies on-screen at once--if the 3D effect is also taxing the GPU. However the 3D effect does work on the more robust New 3DS XL and the standard New 3DS, which is finally coming stateside in some Animal Crossing bundles later this week. Naturally if you own a 2DS you can't play Hyrule Warriors Legends in 3D as the 2DS doesn't have that capability at all.
In any case I don't think this is a huge loss. In my opinion the more stable 3D effect on the New 3DS hardware is the only thing that makes the effect bearable for long periods anyway, and with an action-heavy game like Hyrule Warriors I don't want to think about keeping my older 3DS XL perfectly still during those heated battles.
Source: Nintendolife