I had a chance to collaborate with a librarian that worked for Soundelux for almost almost 15 years. He suggested the best way to organize a library was to be very specific and blunt in the folder structure, such as:
Vehicles: Aircraft, Automobiles, Locomotives, Spacecraft, Water Craft
Then using sub-folders to list each type of vehicle in its suggested master. The glue that holds the entire system together is the meta-data. His goal was to be able to find any sound effect he wanted without having to use Soundminer. So if wanted a laser blaster it would be filed such as: Weapons/Guns/Sci_Fi/Laser
As far as mastering is concerned I label every recording in my 702 before I record it and save the files to my "To Be Mastered" folder that is within my SFX library structure. This gives me access to the files even if I have not had a chance to master yet. I too save the originals to a separate folder outside of my database using the method used above.