During the game, the MC goes to the vault several times due to instinct or something similar (like on the 1st and 3rd), all these times there is really a password to put in, or something just to make the player pay attention , as if the game were saying "there is a reason for this to be here so pay attention".
It's a combination of both, but a lot of people forget that the vault is there to be used.
Originally there was a password for Day 1 that was used for testing and had some off-shoot non-canon scenario where everyone died to being gassed a la Zero Escape style. Day 3 still has a password but that's mostly for testing and not intended for you to get through normal gameplay.