It won't shut down, it'll survive. The only thing that will change is the player experience, significantly. But as you said, the owners have something up their sleeves.
Nope, basically what Mr. Alon said,
you are not allowed to sell in-game currency for real world money.
It's not all just because they aren't getting enough income. It's true they might be using the EULA just to get players to buy their product, AKA realms. But that's not all there is to it.
Mojang's main goal isn't to stop servers from making money, Mojang's main goal with the EULA rules is to prevent unfair extortion and situations like a player-vs-player (PVP) server charging a couple hundred bucks just for a diamond kit or selling OP items that make the game play highly unfair. It is indeed fair, but under those rules, they're also preventing more balanced monetisation strategies.
You can find a detailed post I made found here-
http://www.snapcraft.net/threads/1917/#post-15498