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The article actually says the reason is in the name, which translates as Deep Well.

They just didn’t build below the water table…simple…. They probably improved it by digging the wells good and deep…

Yes, I’m concurring with the first reply.

Or how nobody ever noticed the ventilation shafts.

Prior to mechanically pumped water, wells were within walking distance pretty much everywhere. I believe most/all of the ventilation shafts at least looked like wells, if not doubling as wells.

Maybe, but it seems like a well that doubles as a ventilation shaft for a labyrinthine underground city wouldn't be very good at either job.

Why wouldn't they work well as wells?

They wouldn't be optimal ventilation shafts, but they'd be hidden, and apparently generally sufficient.

By exploiting existing long-established natural underground rivers and water basins ..