I expect it's the shift, paired with a lower absorption level. Like nearly everything about humans, vitamin-D absorption is not the same for everyone, even within "normal" tolerances. Someone with low-normal absorption would be fine with a normal schedule. Put them on nights, and that might be just enough to put them at a deficit.I've worked shifts for over 40 years, 12 hour shifts including a lot of night shifts. I quite like sleeping through the day but you don't sleep through all the daylight hours. You don't need hours of sun every day to get your vitamin D. Our federation had looked extensively into shift patterns and health, shifts do cause medical problems but I would suspect the deficiency is indicating underlying problems.
this didn't apply to us but it did the civilian staff. https://www.tuc.org.uk/sites/default/files/AHardDaysNight.pdf