This is the conclusion of the paper [1] that this article is based upon: "We suggest that any real declines are generally most easily explained by changes in cultivated varieties between 1950 and 1999, in which there may be trade-offs between yield and nutrient content."
What National Geographic says scientists say, "Scientists say that the root of the problem lies in modern agricultural processes that increase crop yields but disturb soil health. These include irrigation, fertilization, and harvesting methods that also disrupt essential interactions between plants and soil fungi, which reduces absorption of nutrients from the soil. These issues are occurring against the backdrop of climate change and rising levels of carbon dioxide, which are also lowering the nutrient contents of fruits, vegetables, and grains."
Modern media in a nutshell.