Why not? It's not like they can just go down to the local HackerNinjaRockStar DojoSpace and rent some Ikea standing desks. At Apple, for instance, there are sealed buildings and security requirements that impose a cost on expansion above espresso machines and foosball tables -- and they're not required to meet DoD legal standards.
This is probably true. Still, it seems like a red flag to me that on a project like the F-35, which presumably has adequate funding for office space and other such things, their only solution for providing offices for their own employees is night shifts.
There's a very good reason not to have engineers work nights. While some are undoubtedly night owls, many (most?) will have lives and families which will suffer from night shifts. That accelerates burnout and increases resentment--both of which are usually running high in a troubled project anyway.