Not really. I have a friend who flew for Cathay. The pilots really liked getting assigned to the freighter runs because it meant they didn't have to fly around turbulence like they did if they had a plane full of passengers - They could just fly right through it and carry on. The main risk of damage is from things like hail, and there isn't any hail at those altitudes.

Here's a video of a US Air Force "hurricane hunter" aircraft flying right into a hurricane:

http://www.youtube.com/watch?v=IxYfl-inCw8

The aircraft doesn't fall apart...