I have read that many users that updated their Wiis with the latest firmware, can still use Action Replay by booting it with GCOS (booting the WiiKey setup disk this way works as well).
As of right now, I can't remember where I read it (I closed the link prematurely), but once I can find it again I'll post a link here.
So, consider this a poll of sorts. If you've updated your modded Wii and have Action Replay, please test it out by booting GCOS first! Then post your results here. I would test it myself, but I haven't updated and don't own Action Replay.
Also, it would be a good idea if some people could test the SD Media Launcher, Freeloader etc... These possibly could work with this method!!!