Maybe it'll be in future in an indie bundle.
I find that unlikely since SMB has been out for a while, also it was already featured on Humble Indie Bundle.
It could be added to the beat the average bonus for future Humble Bundles, it's already happened once before. Humble Bundle does a lot of repeats, so it's definitely possible. I mean look at Machinarium.. that's been in quite a few bundles.
Possible - it has only been in only two bundles to date: HIB4 and HIB5 (last of which ended June 13th).
However, they are probably trying to draw attention to their work as it looks like they are getting closer to their game, Mew-Genics completion (no release date, should be out around Christmas).