A nuclear warhead can be put in a box (made of materials) that can contain its particle emissions, and consequently minimize its chances of detection from sensors that can detect such emissions. However, story does not ends here. Next step is to develop sensors that can detect emissions of the materials of such boxes.
HINT: All objects emit something (e.g. electromagnetic radiation).
I pointed out earlier that different types of systems have been developed and fielded by US strategic forces to detect presence of nuclear weapons and map their storage locations in enemy territory worldwide; its a multi-layered surveillance system. These developments are largely
classified and would not be disclosed to the public in detail (at any cost) because such disclosures can undermine US nuclear primacy.
US may have developed a comprehensive model of Pakistani strategic assets in "laboratory setting." They will continue to update it with passage of time as they notice newer developments. Check this article:
http://fas.org/nuke/guide/pakistan/facility/ (This article contains information about Pakistani strategic areas that US authorities decided to disclose to the public). Now imagine how much information they have in "laboratory setting."
There are different methods to figure out location of nuclear warheads in an area.
I felt the need to diversify my skills.