Pakistan is estimated to have 60 or so nuclear weapons, deployed in "widely dispersed" sites across the country. The dispersal of nuclear weapons is key to Pakistan's deterrence strategy and is in accord with general guidelines for deploying strategic weapons in order to maximize survival in case of a first strike. As Secretary of State Hillary Clinton has pointed out, however, the same deployment that makes sense for Indo-Pakistani relations spells trouble in the context of a growing Taliban insurgency. A larger number of nuclear sites increases the vulnerability of the Pakistani arsenal to Taliban seizure, theft, or sabotage.
As the New York Times points out, the U.S. has strongly supported efforts to secure Pakistan's nuclear arsenal, giving roughly $100 million over the past several years in order train Pakistani personnel and improve site defenses. Predictably, however, Pakistani cooperation has been limited. The Pakistanis remain reluctant to detail their nuclear locations for the U.S., out of concern that the U.S. would seize or attack the nuclear weapons in order to prevent Taliban takeover. This concern on the part of the Pakistanis is not at all unreasonable; I suspect that the U.S. would take very strong steps to prevent nuclear weapons from falling into Taliban hands.
In short, nuclear weapons severely complicate the U.S.-Pakistan relationship. Pakistan has a strong incentive not to cooperate with the most important U.S. requests. At the same time, Pakistan's nukes present a greater potential threat to the U.S. than any other facet of the Af-Pak conundrum. My guess is this: The U.S. has carefully cultivated contacts within the Pakistani military and has identified as much of the arsenal as possible, enabling quick action in case of collapse of the Pakistani government (however unlikely that may be). With luck, no test of U.S. preparations will ever be conducted.
--Robert Farley