Raymond Chen from Microsoft has written a post that probably applies here: Computing the size of a directory is more than just adding file sizes. In essence, he explains that information like the size of a dir cannot be stored in the dir's entry, because different users might have different permissions, possibly making some of the files invisible to them. Therefore, the only way to get the size the user should see is to calculate it upon request from the user.
In your case, the answer probably stems from the same reasoning. The list of directories available to your app can only be determined when your app asks for it, as its view of the root directory might be different than another app's, running with different credentials. Why Windows store directories along with files I don't know, but that's a given.
Since Win32 is as close as you'll get to the file system in user mode, I'd avoid any higher level solutions such as .NET, as it might only simplify the interface. A driver might work quicker, but that out of the scope of my knowledge.