The linked NYT article [1] says it's "well over 100,000" which is a whole order of magnitude lower. But more importantly, it also seems to conflate what is a true bomb shelter, versus what are merely regular basement apartments:
"Nearly every apartment building in the Digua Shequ center’s neighborhood has a former shelter or a basement... If you get rid of these basement units, where will the migrants live?... A lot of landlords have spent money renovating the spaces they lease, so they don’t want to stop renting out basements..."
I mean, c'mon -- people live in basement apartments in Manhattan too, it's not that bad. And then, yes, I could maybe believe that 1/20 people in Beijing lives in a basement apartment if the average building is 10 stories tall with a single-story basement. And that then a much smaller number live in the actual bomb shelters that aren't just basements.
[1] https://www.nytimes.com/2016/03/22/world/asia/beijing-bomb-s...