First, uncertainties associated with changing analytical methods call into question how comparable are 60-year old data vs. new data. That said, it is true that environmental factors such as weather, soil type, and soil mineral content result in variable nutrient content in edible plants. Plant genetics also play a factor, as does post-harvest handling and cooking. Soil depletion is a concern, but farmers have become much better at preserving soil health and optimizing nutrients so they have healthy plants and strong yields that can be sustained year after year. Any gross deficiencies or excesses in soil nutrients for the plant result in a poor crop, so there is plenty of economic motivation for farmers to optimize their soil.
Furthermore, plants can (easily) be bred for higher nutrition if there were a need. One can argue that while old vs. new data may show nutritional composition differences, it likely isn’t nutritionally significant. For example, whether a ½ cup of peppers contains more than the current 140 mg vitamin C isn’t really that important when only 75-90 mg/day is needed by the body in the first place. Seed breeders today have to balance already very nutritious fruit and vegetables with other factors that are also important to consumers, like: improved plant disease resistance, so less use of pesticides, herbicides or fungicides; increased plant productivity, resulting in less expensive food; increased plant stress tolerance to manage changes in climate, ultimately resulting in less expensive food; more attractive fruit/vegetables to increase the desire to eat them; better shelf-life so it doesn’t spoil as fast in the fridge at home, resulting in less waste, and ultimately less expensive food; or better flavor, which increases the desire to eat more.
Ultimately, not eating enough (already very nutritious) fruit and vegetables is much more of a problem than any minor changes in nutritional composition that may (or may not have) occurred over time.