I think it will probably be a bit more complicated than just replacing a few files because the game is linked to specific files that link to other specific files (and offsets in those files) which would all need editing to just replace files. If you were just replacing videos that would be different. Now depending on how far the developers got into the game development before the censorship became an issue, you might be able to just hex a few files and make it work. Start out by opening the xbe in a hex editor and scanning over the whole thing for any reference to "decapitation" "decapitate" "animation" or possible "00000000" or "FFFFFFFF" as these would probably be how they would cancel something out. (At least, thats how bungie canceled out stuff they had originally intended to be in Halo but later removed to speed development.) I'll take a look at the game directories overview in a bit and see what I find.
Most likely the actual decapitation wasn't programmed into the PAL Ninja Gaiden, and if so, it probably won't be easy to incorporate. Your best bet is to see if Gamefly will work in your area and see if you can request an NTSC version specifically and if that doesn't work, get one of your game friends in America (or Japan) to "loan" theirs to you and you pay the shipping.