Retailers were conservative in ordering and/or Nintendo was conservative in shipping the bundle (not wanting more pissed off retailers).
To be honest though if you already have a Wiimote+ your house, the NSMBU bundle + Mario Kart 8 separately is the better buy.
You get NSMBU + NSLU + Mario Kart 8 + the extra free game for about $359.99 US vs. $330 for just the Mario Kart 8 bundle.
NSMBU + NSLU for $30 more is a pretty sound deal.