Interesting...I got a "good ending?" (with the question mark and all) and yes, I can definitely confirm the passwords were hidden well :)) i *think* i managed to find nearly all of them, but it's apparent to me from the ending i saw that there is still more content for me to find...
If you want, a simple, spoiler free and hinting instead of outright answering guide to getting all the endings read below.
Good Ending?: Complete the game without achieving any other endings.
Bad Ending: Fall at the last hurdle.
Secret Endings 1: Find the secret files, input the secret code you get from looking within instead of the one the game asks for. Make a choice at the ending.
Secret Endings 2: Find the secret files, input the secret code you get from looking within instead of the one the game asks for. Make a different choice at the ending.