Ok, the following may be a little far-fetched, but hear me out...
Initially, I thought that Nintendo changed the password system to create a "new" start or fresh playing environment for the game where people couldn't use old passwords to bypass playing the game.
However, when I remembered that one of the "cheat" passwords was something to the effect of "DANGER TERROR !!!!!!" it occurred to me that it may have had less to do with fairness and more to do with eliminating a password that is "non-PC."
There is no hardware reason to change the password system. The password routine is part of the game code. There was no special chip that processed the passwords (contrary to the belief that seems to be spreading).
The amount of attention that has been paid to special ways to fold $20 bills so that they resemble the twin towers burning, the fonts in MS Word that show airplanes and blocks that look similar to buildings, and all the other conspiracy theories may have convinced them that this one password probably should be eliminated.
Otherwise, how long would it have been before someone postulated that the Japanese were behind 9/11 and put that password in as a clue? (why perpetrators of a conspiracy would want to leave clues is beyond me, but see above conspiracy theories)
Anyway, just a thought...perhaps I should stop drinking so much coffee...