Usually bigger monsters, bigger buildings and bigger objects indicate importance.
Boss monsters may reach size of 1/3-1/4 of screen, while smaller 1/6 might indicate unique area monsters. Bigger buildings might host dungeons or important portals/npcs.
Bigger objects may have important activation functions(such as shrines/gates/portals).
Player expects size to represent vague "power", so its better not to assign it randomly by monster type or building/object design(e.g. long sword weaker than a dagger-like weapon).