No it doesn't. You're looking waaay too much into it.
A bunch of Indie Devs have already stated how awesome it is to work with the WiiU, that's why you see so many great titles on the eShop already. This is just Notch being stupid.
I'm probably going to get a lot of hate for this, but Notch talks and acts as if he's god among indie developers. He's fucking arrogant too. Say the Microsoft agreement does expire, and brings Minecraft to PlayStation, why not the WiiU? There's no excuse. He doesn't even say any. When you already see such awesome indie games on the eShop and see devs talk about how awesome it is, this is just Notch being a dick.
But hey, I don't like Minecraft to begin with. It's boring as hell. But this doesn't affect other third party/indie developers at all.
edit:
No they won't. Jesus, you're one of the retarded doomsayers aren't you?