As a headline from the industry publication World Poultry made clear: "Salmonella thrives in cage housing."  A meta-analysis conducted by Pennsylvania State University's Department of Animal Science and published by the American Association of Avian Pathologists concluded that cage housing for laying hens increases the risk of Salmonella contamination.  Just some examples of the published, scientific findings showing higher rates of Salmonella in egg facilities using cages than in those without include:
While these studies evaluate Salmonella at the production level, every study ever published comparing risk at the consumer level has tied Salmonella infection to cage egg consumption: A prospective case-control study published in the American Journal of Epidemiology found that people who recently ate eggs from caged hens had twice the odds of being sickened by Salmonella , for example, and a study in Epidemiology and Infection found nearly 5 times lower odds of Salmonella poisoning in consumers who chose eggs from free-range hens .
Even pasteurized egg products are at risk. As the U.S. Department of Agriculture concludes in its report, Evaluating the Effectiveness of Pasteurization for Reducing Human Illness from Salmonella in Egg Products: "It is reasonable to assume that people become exposed to Salmonella by consuming pasteurized egg products…" 
All the data clearly points in one direction: using or producing eggs from caged hens increases food safety risks for producers and consumers alike.