Nintendo is to save costs on the new Nintendo 2DS console, but the omission of 3D output is just one of the ways.
According to one report, because the Nintendo 2DS hardware lacks a clamshell/folding cover and takes on a more slate-like approach, both screens are actually a single touch-screen. However, the top/main screen is covered by a layer of plastic to prevent touch-screen input, with the actual hardware casing acting as a mask between the two screens.
This means the entire screen is by necessity a touch-screen, with the upper screen protected by a layer of plastic that sits above it.
The Nintendo 2DS, announced today, plays all 3DS and DS titles but does not output to 3D. The console, launching this October, is intended to be a budget/entry-level console for younger players who would like to play 3DS titles - for example the upcoming release of Pokémon X and Pokémon Y.