I'm sorry if this is a really freaking basic question but I'm wracking my brain here. I've had SNES9x-GX working on my old Wii but now the only download link downloads source code only instead of the compiled version, however the readme still talks as if it's the compiled version I'm downloading.

It worked fine before, and I tried the separate Wii channel and it doesn't work. I'd rather have all my emulators in one place anyway (The Homebrew channel). Can anybody help with this?

The compiled code can be found under the Releases tab on the SNES9xGx's GitHub page. The latest version for Wii is 4.3.2. You can find the Channel Installer on that page as well.
Installing the Channel works like a redirect -- the same way a Shortcut icon works on your computer. It's not the actual program. If you want to use the SNES9xGx Channel, you still need to download the program to your SD/USB disk. I had this same problem initially, so I reread and followed the directions on the WiiBrew page and I haven't had any problems since.

Hope that helps! Cheers!