When some horses are locked in stalls for long periods of time, they can become cranky, etc. In longer periods of time they could possibly experience some pains from standing in one spot for a long amount of time.
It's very important that in the winter a horse gets extra hay so they digestive system works and it keeps them warm. Exercises is a must too, eating and exercising can warm a horse's body up and relieve joints.
You also have to know that horses are claustrophobic so being in a place where there isn't much room is going to make some horses aggressive.
Some horses do just fine and don't have problems at all in stalls, but there are some horses who probably shouldn't be in a stall and if they should be in a stall they should get plenty of exercise.