Do you have experience with fiberglass?  It would have to be some kind of an aerodynamic shape or you would really kill your mileage.  I wonder about the structural integrity as well.  I experimented briefly with fiberglass modification many years ago, and the smell alone was enough to turn me off.  Horrible stuff to work with.

I recently added a 2 inch hitch and cargo carrier for example at the rear of the van, and I know some people add those to the front as well.  You could certainly add a mini teardrop trailer or for that matter several Yakima storage containers on the roof.  All these are certainly much easier than fabricating a new shape in the pop top.  Access from the inside would certainly be nice.

Perhaps you're just looking for a project?  It sounds like an interesting idea, I just think there are easier ways to get storage.  Let us know what you decide.

Troy