Is there any documentation from Nintendo themselves in respect to the NES's workings like the PPU or some more detailed hardware stuff?
Yes it exists, and it's been sold, but never scanned and released. Now with the chips decapped it's really only of "use" to collectors. Additionally it's been mentioned by past developers that the official documentation was seriously lacking depth (and some only received a Japanese manual) so I doubt they detail the inner works, patents are the place for that. (What exactly do you mean? You program 6502 in assembly so of course it's going to outline registers. Since when does any official documentation go deeper than that though?)
The PPU was decapped? When did this happen? Have any emulators moved toward perfecting emulation with whatever knowledge was gained?
Well I don't program fo rthe thing but I've just always wondered how complete Nintendo was in describing these things. I guess they weren't very complete at all 3: Oh well
I thought so... Maybe it's just in the pipeline. I think I read Quietust is RE'ing the APU. It probably was pretty rough, but still sufficient if you aren't going to perform extreme raster tricks. Programmers tend to enjoy complaining about support even if they have what they need. I'd really like the document just to know the Nintendo sanctioned names.