Early on in the book the NSA is described as a top secret agency, an agency very few Americans know exist. However throughout the rest of the book there are many references to groups who openly protest against the NSA, bad widespread publicity, and the majority of Americans being against the agency. If hardly anybody knows about the NSA then how can there be so much open debate about it?
The cipher that Brown calls a "Caesar box cipher" is actually called a columnar transposition cipher. Julius Caesar did really invent ciphers, but the only one whose description has survived - and which to this day is called the "Caesar cipher" - is much simpler than the columnar transposition.