No, we’re not getting transparent 3DS systems (yet?), that Nintendo 3DS XL model was just a demo unit shown during an Iwata Asks interview.
While talking about the design of the 3DS XL, Miyatake from the design group explained why the top screen is surrounded by a black frame. This color was chosen because it emphasizes the stereoscopic 3D effect, but with a screen as large as the 3DS XL’s you don’t need to have a black frame anymore. Fujita also said the sound quality of the 3DS XL is a bit different since the 3DS had small speakers those had to be optimized using software. While looking at different speaker options, Fujita used the Dragon Quest opening theme as a test.