Plants growing in soil need other soil organisms to transport nutrients for them. But even in hydroponics, we don't really understand the minute by minute needs of the plant, so we load the nutrient solution with excess nutrients, to the point that water quality is usually extremely poor in a hydroponics system. This leads to water pollution problems that could be avoided if the normal nutrient cycling processes were allowed to occur. The organisms that suppress disease-causing organisms are present. The organisms that degrade toxic materials are also present.
Soil chemistry is right for the plant.
If all the Ca is complexed in forms the plant can't use, the plant will suffer, and generally succumbs to disease because it is too stressed to resist the disease. Salt is an important factor - not too much and not too little. If soil chemistry and soil biology are right, soil will have the right structure - in other words, soil physics will be just fine. Natural disturbances as well as human disturbances can kill these organisms. We need to learn what those situations are and how to encourage and select for the presence of the appropriate organisms to grow the plants we want to grow.