Recent reports on the IRC have said that update 3.4 from Nintendo will delete all Custom Channels. Whether this means that the Homebrew Channel will be effected by this I do not know. I do not suggest updating with anything other than Tona's Updater as it installs updates without patching exploits homebrew uses. You can download the Tona Updater HERE.
edit by mcpancakes: I received (and probably other people) a message from Nintendo on my Wii message board. It talked about System Menu version 3.4 and what it does. You can find the transcription here.
EDIT: The update has been confirmed not to remove the HBC but it is still not encouraged to update.