SPOILER for Cryptonomicon, although the plot is so confusing that it doesn't give away anything significant.
Enoch Root's death was faked. From page 542:
"The doctor stops in at the courthouse to drop off the death certificate.
Otto and Julieta go on ahead to the cafe. Bobby Shaftoe loiters outside, staring back up the street. After a minute or two he sees Rudy poke his head out the door of the doctor's office and look one way, then the other. He pulls his head back inside for a moment. Then he and another man walk out of the office. The other man is wrapped in a blanket that covers even his head. They climb into the Mercedes, Blanket Man lies down in the back seat, and Rudy drives off in the direction of his cottage."
The man beneath the blanket was obviously Root, as he was the only person in the clinic besides Rudy.