The main content of plant-created biomass comes from atmospheric CO2 and water, not from soil (well, roots extract water from the soil, but that's not what we mean by soil depletion). A significant minority is nitrogen, which either needs nitrogen-fixing plants (which extract it from atmosphere) or fertilization.
If the end-product is more carbon and nitrogen, doesn't that also mean it's less nutrient dense in other important micronutrients?
There is a long term trend that vegetables are getting less nutritious, yes. And it is speculated that it is because of soil depletion.