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.
* It's a jobs program to avoid the knowledge loss created by the end of the cold war. The US government poured a lot of money into recreating the institutional knowledge needed to build weapons (e.g. materials like FOGBANK) and it's preferred to maintain that knowledge by having people work on nuclear programs that aren't quite so objectionable as weapon design.
* It helps you better understand the existing weapons stockpiles and how they're aging.
* It's an obvious demonstration of your capabilities and funding for deterrence purposes.
* It's political posturing to have a big supercomputer and the DoE is one of the few agencies with both the means and the motivation to do so publicly. This has supposedly been a major motivator for the Chinese supercomputers.
There's all sorts of minor ancillary benefits that come out of these efforts too.