Well this is a pleasant surprise. According to Nintendo of America's Twitter, Minecraft New 3DS Edition is getting a retail release on November 10th. The box art also indicates Amiibo support, and personally I'm hoping that might give you Nintendo-themed costumes based on the Amiibo you scan, but I'm just blue-skying here.
I thought Minecraft wasn't the best fit for the 3DS as it's currently lacking a multiplayer mode (if you want portable Minecraft, the Switch version is the way to go) but I also felt that standing on its own, it was a perfectly serviceable port. It's nice to see that this version is getting some strong support; there are plenty of great indie titles that aren't getting a physical release, but apparently Minecraft's popularity warrants a retail version.