Why do clouds have ceilings and bases?
Clouds have ceilings and bases because the atmosphere is stratified. 
Atmosphere is stratified due to earth's rotation and variance of composition, humidity, density,  temperature, and pressure from surface of the earth to the edge of the orbital space.

Clouds form under specific conditions of composition, humidity, density,  temperature, and pressure.  These conditions are often persisted within specific layers in the atmosphere.  Complex fluid flow of air is also a contributing factor for layering within the atmosphere between air masses for varying density.

The answer is probably best summed up as the result of the physics of fluid dynamics.