Tons of folks on social media had theorized that the reason for Nintendo's decision to pull the repackage from stores is that the company is seeing how much of a demand there is for these old-school Mario titles.
And with the "always-on" connectivity of games, especially digital titles, Nintendo gets real-time metrics on player usage.
In other words, Nintendo knows which of the three titles gamers are playing the most from SuperMario 3D All Stars, which could mean that they've found out which games from the pack are worth dumping more marketing dollars into. Perhaps they do indeed intend to earn more revenue down the line by selling the games as standalone titles.
The good news is that if you want the game, it's still available until the end of March, and there might be a good chance you can still find used cartridges in stores across America after that. But the resale on those bad boys might get really high, so act fast.