Club Nintendo and HBC

If I update my Wii and link it to my Club Nintendo account, will Nintendo be able to find out that I have the Homebrew Channel? Also, if they can find that out, how would they respond? If I wanted to redeem a WiiWare game with Club Nintendo Coins, do I need to have my Wii linked to my account to receive the game?

It is perfectly safe to connect your Wii to your Club Nintendo account. Mine is connected to mine, and I have had no issues. Nintendo probably can find out what you have installed, but to date they have done nothing with that information. (There is even a channel called the "Nintendo Channel" that to use, you have to agree to send your play logs to Nintendo. Back when Homebrew Channel appeared in play logs, I often had it in my logs when they were sent off to Nintendo. They never did anything about that either).

Of course, they could start doing something, but the worst they can legally do is either remove HBC or block access to the Shop Channel. They can't "brick" your Wii or anything like that, that'd be illegal.