Simple answer. No. You can spread scenes over multiple documents. And, using the techniques for "accessing scenes from inside and outside Hype" (search for the relevant post here), you can perhaps access the relevant scenes (document) as and when you need it. Can't really elaborate more as I don't know your setup. May take a little work to get it as you want it. Data gathering and saving would become a small issue when doing this.
Thinking out loud. I would just have one conclusion scene and dynamically change the data in it based on the user. Again, not knowing your setup I'm not sure what's being included in those scenes.
Unfortunately no. But, there is a way when advance exporting to create a folder structure for assets I believe