With the rarer NES games, the manuals will generally be worth more than the boxes. They are expensive because they are just super-hard to find, especially hard to find without rental stickers. Alot of rental stores would keep the boxes but somehow end up destroying the manual or throwing them out. People want them complete in the box, and many boxed nes games have the habit of showing up without manuals. Ive been looking for a little samson manual (reasonably priced) for at least 8 years.
It really doesnt matter if scans are available on the internet, people want the originals to complete their collections. I dont think anyone will spend 100$+ because they need to read how to play a nes game..