I see no issues with the concept. Zenphoto shouldn't know/care about the fact that it's symlinked as log as you don't move the folders all the time. For what you'd like to do I'd say this is an excellent idea. I'm personally a huge fan of symlinking, it's how I map all my local webhost folders on my PC for testing without having to traverse through my root structure all the time.

I say if you're on a Linux server you might as well take advantage of the benefits. Just make sure you never get accidentally migrated to a windows machine