Most torrents will tell you in the header whether the game is scrubbed or not. You can also tell by the filesize: If it's lower than ~4.37GB in size then it's probably scrubbed.
You'll generally only need to worry about scrubbing updates if you're loading from disc. Usb loaders wipe the update partition when games are added to WBFS drives. The software you're looking for is either Wiiscrubber or Brickblocker, the former being the most popular and both easily found via Google.
You can also use a hack in Priiloader or Startpatch to prevent disc updates from ever showing up.
So far any update prompt asks for your permission before updating the system.