As I get deeper into Cryptonomicon, Bobby Shaftoe seems to remind me a lot of Hal Incandenza. Beyond his moments with Glory (which he promptly sets out to forget), Bobby has an automated robotic and detached quality about him. Beginning with the lizard incident, he feels unable to communicate with others except in his military protocol which Stephenson essentially boils down to a sterile enabler for the less pleasant side of soldiery i.e. killing other people. As we see on page 203 Bobby misses the "good old days, back on Guadalcanal" where he was "a free agent" able to accomplish his orders by all means necessary, but now he just takes exact orders with absolutely no freedom. Even more telling, as we encounter the scene in the captured U-Boat, Shaftoe wants to bomb the safe not to accomplish his orders but to get more morphine. Where he once took pride in his work, all he wants when he receives praise for his work on the safe is to find some private place to go take his morphine on p299 (remind you of Hal and his Bob Hope at all?).
Shaftoe seems content in his military lingo. I vaguely remember him saying that it's a very efficient way of communicating. But then he gets frustrated with his lack of knowledge about what he is doing and he goes to talk to Root about it, and he seems to be able to use military language to his advantage. He seems to know how to make it useful despite it's utilitarian feel.
"Shaftoe gets the skipper really pissed off by asking him three times whether he's sure he has the order worded correctly. One of the reasons Shaftoe is so highly regarded by the enlisted men is that he knows how to ask these kinds of questions without technically violating the rules of military etiquette." -page 374