Gecko codes were never supported in GameCube games; they only worked due to a flaw in the code design. When features were added to Dolphin, the flaw was fixed and now the correct behavior (well, not correct, we never want Dolphin to crash) for the current system happens. What needs to be happened is setting up a proper GameCube Gecko codehandler, and no one has had the time to implement it yet.
It will be fixed before the next release in all likelihood, as it is a regression from 4.0.
It will be fixed before the next release in all likelihood, as it is a regression from 4.0.