Your second sentence "rates and power substations ... to cancel operations" is not right. It seems to be missing some words. However, I can still try to answer your 2 questions: (a) crack down, (b) rates on power substation.
a. The phrasal verb "crack down" has a direct object. If the direct object is a person or people, then "crack down" means to treat them aggressively. If the direct object is some type of crime, such as the thefts of metal, then "crack down" means to investigate the crimes more aggressively.
b. The meaning of "rates in power substations" depends on the context. The first sentence refers to "the rise in thefts of metal": this is the context. In this context the word "rates" in "rates in power substations" refers to the rate (or frequency) of thefts of metal, and "rates in power substations" means "frequency of thefts of metal from power substations". When a thief removes metal from a "power substation", the power substation cannot function properly. Some of these power substations are hospital generators. When a hospital generator stops working because a thief has taken some of the metal, doctors must cancel operations.