On July 15/16 Nintendo release a new update, 4.1. As per Nintendo's patch notes, there was no major updates to the system, but they did make "Improve System Performance".
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While I seriously doubt there was an imporovment in the performance of the console, I do feel this is a poorly disguised effort to attack Wii modifications.
I have done some research and it appears to only affect the following:
Twilight Hack (successfully stopped by Nintendo)
Homebrew Channel (partially successful)
DVDX (partially successful)
And copy-protected copying of some savegame files (largely successful).
So it would appear, for now, that hardware modifications are still safe.
Please let us know your experiences if you have already updated to 4.1. Feel free to add or correct any information you KNOW is accurate. Thanks!