Notch has been in very close contact with the players of the game throughout development, and has a keen sense of what this mass of people is looking for.
If you can show that Mojang does TDD, 'story' card walls, velocity tracking or kanban pipelines or any of the concrete "developing practices" (to use your term) pushed by the agile consultant folks (vs some motherhood "values" that can be retrospectively applied to any successful project try say Google+ instead of MineCraft and you could call it an "agile" success story too) then you'd have more of a case.[1]
Otherwise you could label any successful project anywhere "agile".
[1] I am not saying Mojang doesn't do "agile". Maybe he does - in which case a comment that explained which concrete practices he found useful would be great. I am just tired of agilists latching on to any and all successful projects and calling them "agile" to the point where "agile" becomes a synonym for "successful".
I'm just speculating of course, as are we all. Just saying that from my perspective, they don't look like a team using agile practices. They don't look like a team using any kind of standard industry practices at all, really.
Disclaimer: I love Minecraft, play it all the time.