Well, FSF and Remi notified Apple of the situation, and Apple removed them (GNU Go, Battle for Wesnoth, VLC).
As I understand, FSF and Remi did not request Apple for removal, they requested either Apple modify their terms of use to be compatible with GPL, or failing that, remove the app. It was Apple's choice.
EDIT: the parent added question about App Store terms change after I replied. I am working on that.