Figure Source: https://bit.ly/2XzS8tD
Figure: Problem of salinity
Yes, permanently submerging roots in water is a bad thing for all but aquatic plants. But, it turns out that if you bubble enough air into the water and keep it at the right temperature, roots will thrive. Add some mineral-based nutrients and you have a powerhouse hydroponic growing method!
Only bare roots should be submersed, up to the base of the rooted stalk. Do not allow the stem to become submerged.
Yes, root diseases are one of the major problems that you may face. If you see the roots start to turn dark brown/black. Warm water, high nutrient strengths and dirty growing conditions are the culprits.
A well-hydrated plant typically grows incredibly fast and growers should adapt by shortening vegetative times by around 15-25%.