But the strangeness was that the pp Store even looked at my clones... Should have stuck on the Boot drive...

Why?

I think it's probably designed to look for apps on all attached drives for which there is an Applications folder in the root directory.

Allow me to suggest that you should NEVER have your clone drives mounted, except when you're actually cloning, or trying to restore something from a clone.

There's no benefit to having them mounted at other times, and a hundred ways to screw things up if they are mounted. For example, lots of updaters (not just the Mac App Store) will look for any copies of an app they're supposed to update. Or you might use spotlight to find a document, and accidentally edit the copy on the clone. And your edits will disappear the next time you do your clone backup.

If those drives are internal, I'd write an AppleScript (or Automator action) to automatically unmount them at boot time.

(In OS 9 you used to be able to set a bit on the drive that would prevent it from auto-mounting at startup, but that doesn't seem possible anymore.)