Start with just water and then progress up to alcohol as needed if there's a tough or especially oily bit of dirt. The water will be gentler to the coating on the silicone and to the rubberized coating that is on the plastic. I've never seen alcohol harm it, and we clean them with alcohol sometimes at KMI, but at the factory where they're made, I notice they clean them with water before they package them up.
Regarding permeability, this video might provide some amusement in case you haven't seen it:http://www.youtube.com/watch?v=s-SwEmg3lGU
The silicone under the plastic is all one big piece, so it should do a pretty good job of keeping the liquid away from the PCB. The most likely danger point is the USB receptacle, if you get liquid in there you might short something out or if you submerse it in a lot of liquid (like accidentally drop it while you're playing in the bathtub, or rescue it from a sunken ship) you should try to let it dry out completely before powering it back up.