Why does it matter where the files "really" are???
Well, suppose the data is spread across several hard drives, including external drives. One day I want to take some of the files with me. Would be quite useful to know, which external drive are they on, right? Especially if "taking them with me" basically means slipping the external drive into my bag.
Now, more to the point of the thread, I do not understand people's frustration with libraries. I understand that some people do not like using them. I have only recently started using them myself. I found them to be useful for the multitude of photos on my computer, but at the same time they don't help me with my work at all.
But, the good thing about them - libraries are not real files, just links, so if you don't like them - don't use them, that's all there is to it! If you are so frustrated with the extra line in the navigation pane, then use Brink's tutorial and remove it.
If you are frustrated that explorer opens in libraries by default, then simply point your shortcut to %windir%\explorer.exe /n,/e, E:\home or whatever your favorite folder (instead of E:\home) - it will automatically go there when you click on the shortcut.
Organizing your data is your personal task. Everybody has their favorite way of doing this, there are no universal recipes - it all depends on what data, how much data, how do you like accessing your data, etc. Libraries is just one of the new ways to do this. Nobody forces you to use them.