Cryptonomicon is essentially about hidden information. Early in the novel, the Japanese bury a large quantity of gold beneath the jungle in the Philippines, then slaughter all the workers who participated. The location of the gold, in a series of secret tunnels called "Golgotha," later surfaces in encrypted messages.

Many of the book's central characters possess knowledge that they must not share. When Randy Waterhouse speaks to the Dentist, for instance, he must be careful not to divulge what he knows. In the same way, Randy's father, Lawrence, at one point refrains from speaking to any of his colleagues lest he inadvertently reveal sensitive information. Bobby Shaftoe, on the other hand, is unfailingly taciturn, though he is never told the purpose of his missions.

Randy also has terrible difficulty in communicating his feelings to Amy, barely managing to tell her that he loves her. His girlfriend, Charlene, publishes a monograph on the subject of beards because she doesn't like Randy's, demonstrating the couple's inability to express any kind of emotion to each other. This contrasts sharply with the effortless communication between Bobby Shaftoe and his girlfriend, Glory, and recalls Lawrence Waterhouse's complete inability to speak to his future wife when the two first meet.

The two time periods in the book are linked by two generations of Waterhouses and Shaftoes. Bobby Shaftoe carries his son up and down the massive steps of the Church of San Agustin in Manila in an attempt to teach him a life lesson, and his son later becomes the owner of the diving firm that Avi and Randy hire. Lawrence Waterhouse, who knows everything about encryption, is superseded by his son, Randy, who becomes an expert hacker. The enigmatic and seemingly immortal Enoch Root, meanwhile, is present throughout the book. Root also appears alongside Shaftoe's and Randy's ancestors in Stephensen's novel Quicksilver, which is set in the late seventeenth and early eighteenth centuries.

Stephensen tells his tale in the well-cadenced style of writing for which he is known. He uses metaphors well in his descriptions of both characters and settings, and he judiciously mingles flashbacks and modern-day scenes in order to maintain the story's pace. The scope of Cryptonomicon is epic, both in the geography it covers and in the stories of its characters.