Many things in Yume Nikki are monochromatic. What this represents, like much of the rest of the game, is up to interpretation.
The White Desert and all its inhabitants are monochromatic, as is Masada and his spaceship. A lot of these parts in the game tie in with the body themes frequently seen in the game as well.
Fan Speculation
One possible interpretation for the monochrome scheme is that is symbolizes past events, much like how we use grayscale to symbolize something in the past nowadays. The occasional red bits found in these black-and-white areas are meant to draw attention to a certain thing, such as the blood coming out of the Severed Heads.
Continuing with this theory, the White Desert's monochrome design could be suggested as a representation of past events in Madotsuki's life. In these speculations, Monoko and Monoe are typically seen as siblings Madotsuki knew before shutting herself off from the world. Monoko is argued to be a girl who was injured or killed in a car crash, represented by her body having bones out of her body (among other injuries) appearing when the Stoplight effect is used. Monoe doesn't react in the same way as her sister, instead disappearing when talked to.
Trivia
- In the files of the game, there are sprites of a monochromatic Madotsuki that are used for her ghost found in Mini Hell. However, alongside the other mugshots for the effects, there is one featuring this appearance. This has lead to speculation that originally, she was going to appear like this while in the White Desert, as it does not have sprites for the FC Worlds.