When they announced the disc version, they said it was a limited edition. Considering there's a bundle with Mario & Luigi U combined on disc, they might have meant it. It might eventually be considered scarce, or it might become like a loose Duck Hunt, ya never know.
They never said it was a limited edition. They said it was available for the Year of Luigi. People on the internet took that to mean it would be discontinued at the end of the year when the Year of Luigi was over. The rumor caught on, and even big sites were reporting it was limited. But as far as I know, Nintendo has never stated that it's a limited edition.