Why can't hot water break disulfide bonds when the energy storage in hot water exceeds the bond energy?
Chemical reactions do not simply occur because there is enough energy around to make something happen. They also require a mechanism that enables something to occur. It isn't enough that the product will release energy on some reaction happening. 

Some reactions will happen spontaneously with enough input of thermal energy to start them off (burning coal, for example). Others, like breaking disulphide bonds) will not. Even when there is a plausible mechanism for a reaction, you have to add enough energy to make the reaction happen which may be much more energy than you expect. Most reactions have an "activation energy" to get past the barriers specific mechanisms holding back the reaction.