no. you do not install shocks opposite of the way they are designed to be installed. I am not worried; It's a $13 shock, and all the wheeling I've done until The 'Con, it hasn't caused a problem.
The only reason shocks need to be mounted the way they were designed is for clearance or mounting style. That being said, if clearance is the problem and you're willing to install new shock mounts, then by all means go ahead and flip em.