Updating won't remove HBC, or BootMii/IOS. If you are already on 4.2, it won't remove BootMii/boot2 either. If you're on 4.1 or below, BootMii/boot2 may be removed if you have it, but you can easily reinstall it.
If you don't want to update though, you can manually update the Shop Channel by using NUSD to download the latest revision and pack it to a WAD, and then use WadImport to install it.