Mood sets the tone that the game is in and the feelings that the player is supposed to feel. While mood can change, the atmosphere is what tells the mood how far it can go in what directions. Mood is different from mechanics in that it is purely visual. While it can affect the mechanics, as in what they do in relation to the setting, they do not affect how the mechanics actually play.
Hollow Knight's mood is that of an almost abandoned world that has been long forgotten by outsiders. While the game isn't super dark, it rarely has bright moments that aren't meant to be of importance. Every enemy is diseased, and every boss is huge and intimidating. The world and characters do not just imply that something horrible happened here, but shove it in your face with enemies such as the Broken Vessel and NPCs such as Hornet. The overall atmosphere is one of perseverance in a crumbling and cruel little world.