Mycorrhizae are perfectly happy in a hydroponic system. But you are right, there are many things we don't understand and some growers don't do things correctly that we do understand.
Many of the modern varieties of mass-produced produce have been bred to overcome pests and harsh conditions. not flavor. By moving the plants indoors we overcome both issues and can grow in optimal conditions where we can focus on taste and texture. Plus by growing close to the point of consumption the food is fresher and tastier and can be harvested when ripe and not a week before so as is currently the case. Additionally the nutrient levels in CEA (Controlled Environment Agriculture) crops is usually above a field grown crop (https://well.blogs.nytimes.com/2016/12/23/are-hydroponic-veg...)