They contain lots of good nutrients however also have toxins such as saponines, phenols, enzyme inhabitors and alkaloids.
Solanin, found mainly in green potatoes and in unripen tomatoes are found to have a toxic effect on digestive system, causing stomach aches, cramps and loose bowls. Combined with saponines they are found to have an ability to block activity of enzyme in nerve cells. If the activity is too strongly blocked the nervous system control of muscle movement can be disrupted.
Another main alkaloids found in nightshade vegetable is steroid alkaloid. The problem with this is the alkaloid involves damage to the joints caused by inflammation and altered mineral states. Some researches found that nightshade alkaloids can contribute to excessive loss of calcium from bone and excessive depositing of calcium in soft tissues.
For these reasons many individuals with joint problems and concern for their wellbeing avoid these foods.
If you suspect if your consumption of nightshade vegetables are contributing a health problem, try eliminating them for 2-3 weeks and see if it improves.
Even if you are not currantly experiencing any effects form these foods, it is a good idea to cut down on the amount and especially careful with potatoes.
Make sure you are not consuming any of the green spots and they had not been waxed. (waxing the potatoes can increase potato decay by cutting down on gas exchange in and out of the potato.)
Cooking the nightshade vegetables is a good idea, reducing the amount of the toxic alkaloids. (though only 40% or so)