NES for example is 256x224
I have programmed games for the NES, and I can assure you that the NTSC NES picture is 256x240. The Super NES is most commonly 256x224 with the black borders you mentioned, and the Sega Genesis is 256x224 or 320x224. On these systems, the size in pixels of the part of the signal that fills the 4:3 frame is 280x240 (or 350x240 in the case of 320px mode on the Genesis), including some borders at the sides that most TVs cut off. The borders would be included in the video uploaded to YouTube, and these borders would still be smaller than the top and bottom borders on letterboxed videos that I see so often on the service.
480p is so-so, at least you have a full video pixel for each original, but the edges doesn't align so it's a bit jittery/blurry.
The nominal bandwidth of a composite signal is 4.2 MHz. The Nyquist rate for a 640-pixel-wide sampling of a 480i component signal is 135/22 = 6.136 MHz. So ideally, one would sample the NTSC signal at 640x240, line-double it to 480p, and let the encoder sort it out. But YouTube punted on this and allowed 60 fps only for high definition, causing flicker transparency effects in these classic games to be rendered incorrectly: either fully opaque or fully invisible.