If I remember correctly, Nintendo's fixes for these hacks were already there in a firmware update late March, a few days after the Freeloader was released. There were just not activate yet because the menu itself wasn't updated to the new firmware.
It was obvious the menu will be updated someday and the Freeloader would then stop working. Anyone who bought one after this late March update should have been aware of it.
When I saw the first few lines of description of the update saying it updated the menu, I knew that was it (although it doesn't affect me as I don't own a Freeloader or ever used any hacks).
It's perfectly normal Nintendo fixes those hacks. Some already manage to use them to pirate Virtual Console and WiiWare games. And eventually such hacks could lead to some cheating, which would be really bad for online competitive stuff.
