It is virtually impossible for US alone to capture or destroy all the nuke warheads. What if, some of the warheads are stored in POK where PLA is present, US is not gonna try any operation out there, as it will be like having a war with China -PAK combined.
Only possibility of grabbing the most of warheads is to have revolt in PAk Army & the rebellion faction comes in support of the operation.
Frankly speaking, firstly, US is probably the only nation that knows where exactly all Pakistani nukes are stored since they have provided more than hundreds of million of dollars in securing those nukes. There's hardly anything that Pakistan can hide from the US.
Secondly, even if nukes are present in POK, the US can still take them out or seize them, and PLA can't do squat about it ! PLA is not a fool that it will engage with US forces when they are themselves in a foreign land ! And if PLA elements are present in a place where Pakistani nukes are stored, then that will certify the fact that China is openly helping Pakistan in its nuclear programs which is against NPT to which it is a signatory.
Third, its no where mentioned that the US will seize them and take them away, they can simply put American special forces in place of Pakistani troops to guard some of these facilities, with substantial aerial support for temporary periods till they safely transport or dispose off those nukes outside Pakistan. Or they can suppress them completely by firing heavy fuel-air warheads directly over those locations from anywhere outside Pakistan.
And believe me, with the kind of resources at its disposal, it can surely carry out such an operation, albeit with some initial difficulties even without India or Afghanistan's help.