Yes, handcuffs are an effective tool for containing inmates when used properly by police officers and staff. The only time they are not effective is when they are misused and cause pain or discomfort for the inmates. Other than that, they keep the hands contained since they could be used to harm those in control.
Handcuffs are an effective tool for containing inmates because it limits their range of motion not only with their arms, but also with their legs as the handcuffs put the body in an unusual position so it is difficult to run away. While possibly uncomfortable, they are not severe nor leave any lasting damage.
It is can hard at times to try to strike a balance between effectiveness and cruel and unusual punishment when trying to detain prisoners. When it comes to handcuffs, I think they do a good job in keeping the prisoner constrained, while not hurting them at the same time. It would be hard to find a tool to replace them.
No, handcuffs only restrict the upper body of an inmate and are not effective at containing inmates. The entire lower body of the person is still fully mobile, and the upper body can still be mobile if the handcuffs are not used properly. An inmate can still run, kick, and perform many other defensive actions while handcuffed.