Is there a way to hide the runes when they are all fully charged and you're out of combat, and show when either in combat or not fully charged?

More appropriate place to ask this is on the WoWInterface forums, but what the heck.

You can add a PostUpdate to the Runes element and hide/show them (using alpha) based on the 6th parameter (runeReady).

As for my layout supporting this I would like to refer you to the locked comment section on the project page on WoWInterface.