Easy questions first: certainly you can have a folder structure under the workspace folder, and that's what the Frequently Used Subfolders are for. They don't have any special function beyond convenience for single-click access.
Library folders generally refer to shared resources, as you suggested. Important distinction, though: files in the Library are treated as read-only by Inventor, similar to the Content Center folder. I think that having an intelligent folder structure in your library would make a lot of sense.
Included Files are just that-- folders that are not under the Workspace but which you want to have readily available to your project. You might include another project temporarily, while you're borrowing concepts or actual files from that project, or it might be permanent. It could be that your project is working on a major component of a large assembly, and that your project would include the top-level project so you have access to attachment points or other common parts of the whole machine. If you have a somewhat complex library structure, you might even define that in a project file, then include that file in all the normal projects, so if something changes in the library structure you only have one file to change, and all the others get it immediately by reference.
Hope that helps.
Here's a lowdown of how I structured our stuff here. This is kind of a hodge podge of different suggestions from posts here.
We have a server folder structure like this:
and so on.
I also have this for vendor stuff:
Z:\Vendor CAD\Vendor 1
Z:\Vendor CAD\Vendor 2
Z:\Vendor CAD\Vendor 3
So for each customer, I created this:
Z:\Customers\Customer1\_PROJECT FOLDER TEMPLATE_
And in that folder, I placed a generically named IPJ file, and a typical subfolder structure for our internal files. Within the "dummy" IPJ file, I added a library link to the Vendor CAD area and any other libraries that I need *READ ONLY* access to.
So when I start a new project, I copy that WHOLE dummy project folder. I rename the copied folder, rename the IPJ file, then activate it in Inventor and I'm ready to start drawing and I've already got the correct folder substructure in place for the project.
On another note, as you're adding new vendor content as things come up, you'll also have to make yourself a project called "Vendor Parts" that has the appropriate work space folder. When you need to make ajdustments to vendor parts, activate that project and you'll have write access to everything.
On yet another note, I even made a folder under each customer folder for a CAD library, such as:
I did this because there are times that we may have multiple projects based around the same customer product model. So I didn't want to have to duplicate each product model for a customer's widget in *every single* project folder. So within each customer's Generic IPJ file, I added a library path to that particular customer's CAD Library. Then I would only have to have one part model for each product that we used.
Hope this helps.
Inventor 2013 64-bit SP1.1, single user
Win 7 Pro 64-bit SP1
Looks like a logical and efficient structure to me. Very similar to how we do ours, except we don't have a vendor library, since nothing is shared between projects-- each one entirely self-contained.