A few years back, during the September Pin Celebration, I know they kept us all inside World Showplace during a warning/watch (can't remember which it was). I don't know what they did with park guests in general at EPCOT during the warning/watch. When the danger was over I remember the park being empty, it may been the heavy rains though. I was suprised that they had Illuminations that night, and you could have the pick of anywhere to see them.
I know Disney has a pretty darn good emergency plan. I'm sure they would make CM only areas accessible in an emergency. They could utilize a lot of backstage that the public never sees.
I have only been there for the one watch/warning, I'm sure someone else hear can shed more light on the subject.