Three main reasons for this are breeding, age and health. Some species breed a lot better when they are away from the public (Guam rails are an example of this at my zoo). The age of animal matters as well. Certain individuals in a way "retire" from public display because of advanced age. Cleveland is doing this with their lone Nile hippo and Philly did this with their elderly jaguarundi. Also if an animal has an illness, injury, or gives birth a zoo might keep them off display until they recover.