Nope, they're separate.
When you go into the Wii Data screen, it makes you choose to look at the channel files or save files. The VC games under Channels are the game data, and fairly large. Then under Saves each game has another file, usually only 1 block for VC games (but stuff like Brawl can have huge save files). For old games without real saving, I think this is where the VC save state goes too.
When I "clean the fridge", I usually move the channel and save both to the SD card, then delete them from the system. But since the Wii has horrifically slow SD transfer speed, it might be smarter to just save the save and redownload the game when you next need it. I just put everything to SD so it's easy to remember what I own that's not currently on the system.