Are they trying to model every single atom?
Is this a case where the physicists in charge get away with programming the most inefficient models possible and then the administration simply replies "oh I guess we'll need a bigger supercomputer"
The alternative is to literally build and detonate a bomb to get empirical data on given design, which might have problems with replicability (important when applying the results to rest of the stockpile) or how exact the data is.
And remember that there is more than one user of every supercomputer deployed at such labs, whether it be multiple "paying" jobs like research simulations, smaller jobs run to educate, test, and optimize before running full scale work, etc.
AFAIK for considerable amount of time, supercomputers run more than one job at a time, too.
So in order to verify that the weapons are still useful and won't fail in random ways, you have to test them.
Which either involves actually exploding them (banned by various treaties that have enough weight that even USA doesn't break them), or numerical simulations.