The black boxes are meant to be another warning for parents, on top of the colorful CERO labels on the spine and the CERO stamp on the cover. This packaging may actually have a benefit too since these games will standout against the basic white box art.
Nintendo seems willing to help warn parents, and point out to gamers which games are mature and which aren't. Currently this is only in Japan and will apply to games rated by CERO a C, D, or Z rating (basically, Teen and up). I'm hoping this comes to North America soon, I'm tired of looking at the white boxes. Also, I think black is a better color anyway. Not as good as red, of course, but less of an eye strain than white. :D