What are the passworded >[???????] pages? Do I have to read further into the story to find the passwords, or should I already know them by the time they come up? One says "1F YOU DON'T KNOW TH3 P4SSWORD Y3T, 1T M34NS YOU'R3 NOT SUPPOS3D TO", so is that implying that I should return later? Or am I just terrible at finding secrets?

You have to read further into the story to find the password. If you’re just now seeing those question mark links, don’t worry about them, they won’t be relevant for awhile.