Well, as strange as it might seem, Nintendo issued a press release stating that their „old“ logo where Nintendo is painted in red is not their official logo for some time – the same logo in grey is.
We’re a bit mystified as to why would anyone attempt such a Don Quixoteish tilting at “logomills”, especially knowing that no one cares, especially the color blind, but there it is.
So we’ll try to heed Nintendo’s advice on using the grey logo in the future, but don’t mind if we slip, as all we care about is the quality of their products. As for the logo, we'll quote one user from Kotaku.com: "Hey, as long as it's not white!".
You can read the press release here (in German).