Well, if one goes looking for symbolism, I find it interesting that the thoughts of the Whisperer are at first transmitted through technology:
This child's voice is currently being transmitted on every television, radio, and cell phone in the world [...] although in an important part of every mind this child's messages are being heard, understood, and taken seriously, in another part - the part that is aware of itself - the messages remain undetected [...] "Is that why your test asked whether we liked television and radio?" asked Reynie. Mr. Benedict tapped his nose. "Exactly [...]"
The Whisperer - and Mr. Curtain - are all about hiding the fact that they are persuading people, tricks, sleight of hand, and removing all thought from the thought process.
One might almost take it as symbolism for how ads and other media are persuading us to do things without our realizing it through our smartphones and other technology. For example, in the study Unconscious processing of Web advertising: Effects on implicit memory, attitude toward the brand, and consideration set, the abstract says:
Consumers have become increasingly savvy about technology in recent years, and many of them ignore Web ads during online activities. In this context, measuring advertising effects based on the traditional cognitive models of information processing may undervalue the effectiveness of Web ads. This study experimentally examined the effects of unconscious processing of Web ads by manipulating the level of attention paid to the ad (directed vs. nondirected attention). Online advertisers should be encouraged by the findings of this study. The results suggest that, upon exposure to Web ads, consumers experience priming caused by implicit memory and build a more favorable attitude toward the advertised brand regardless of the levels of attention they paid to the advertisements. Furthermore, those who unconsciously processed Web ads did not remember seeing the ad explicitly, but they were more likely to include the advertised brand in the consideration set than those who had no exposure.
This seems very similar (in method/effect) to the passage from the Mysterious Benedict Society. See also this article in agreement with my analysis.
It is said in the beginning about the emergency:
Things had gotten desperately out of control, the headlines reported [...] citizens everywhere were clamoring for a major - no, dramatic - improvement in government.
It is all fabricated by Mr. Curtain, who plans to solve the world's problems and become M.A.S.T.E.R. of the Earth and its regions. This seems like some sort of political jab, though I can't really find anything at first glance to to back this up. I'll keep searching.