I can think of at least one situation where red or blue lights would be needed throughout the boat, that's during attacks at night. If the crew has to abandon the boat or get on the deck to operate the deck gun, they need to be ready for it.

If Das Boot is used as any kind of reference (should be accurate btw), they tended to use bright lights even at night when there was no enemy threat nearby, or when they needed good bright illumination in an emergency (when working to fix the boat and get it back on the surface at Gibraltar). In my understanding any boat would have to rig for red when the periscope is used at night or even dark, because the light could be seen far away via the top of the scope.

I don't know what the meaning of the blue light is. I know that in modern subs it's used in compartments where a partial night time lightning is required but red would be inconvenient, such as the sonar room on 688-class US subs. (Because of the periscope issue) I could imagine that it used to be a some kind of an attention light, just like someone mentioned, or maybe an indication of battle stations. I'm not sure if I remember correct, but I think it was switched in in Das Boot when the firing of the torpedoes was authorized.