There is limited research on the overall nutritional effects of pre-soaking dried beans. But the available research points in two clear directions.
The first area of research involves the oligosaccharide content of the beans. Oligosaccharides are a type of carbohydrate that leaches into the soaking water in significant amounts. The loss of these oligosaccharides (like raffinose and stachyose) from the beans into the soaking water has at least two possible consequences. First, it may increase the digestibility of the beans because these compound sugar molecules can require extra work on the part of our digestive tract. This increased digestibility can also mean less gas formation since bacteria in our large intestine can break these oligosaccharides down into gas (carbon dioxide) and water. Second, however, this loss of oligosaccharides from the beans will mean fewer oligosaccharides reaching our large intestine and serving as an energy-source for bacteria like Bifidobacteria or Lactobaccilli that live there. Since full, robust concentrations of these bacteria are usually helpful to our health, this loss of oligosaccharides may not be desirable from an intestinal health standpoint.
If you are trying to minimize the impact of eating beans on your digestive tract, or if you are sensitive to beans from a gas-forming standpoint, soaking beans and losing some oligosaccharides might make sense. If you have a robust digestion and no problem with gas formation, you may want to avoid soaking the beans in order to preserve their oligosaccharide content.
The second area of research involves nutrient loss that takes place as a result of soaking. The overall difference between the nutrient content of soaked-cooked beans versus cooked-only beans does not seem great. Among those nutrients that were lost, many could be found in the soaking water. Even so, I believe it is better to discard this water rather than reusing it when cooking the beans. That's because some dried beans (like red kidney beans) release potentially toxic substances into the water when soaking, and most beans release oligosaccharides, as previously discussed.
One nutrient that does show somewhat greater loss from cooked-only versus soaked-cooked beans is protein. That's because soaking reduces the beans' cooking time; therefore cooked-only beans will be exposed to more heat. This prolonged heat exposure further denatures proteins found in the beans. The overnight cold water soaking method has the advantage of shortening the total time of heat exposure when cooking the beans and reducing nutrient loss in this way.
To soak beans, I recommend placing them in a bowl of cold water and keeping them in the refrigerator for eight hours or overnight. The cold temperature of the refrigerator will keep the beans from fermenting. Before cooking the beans, drain the soaking liquid and rinse the beans well with clean water.
Barampama Z, Simard RE. Effects of Soaking, Cooking and Fermentation on Composition, in-Vitro Starch Digestibility and Nutritive Value of Common Beans. Plant Foods Hum Nutr. 2005;48(4):349-65.
Bornet FR, Brouns F. Immune-Stimulating and Gut Health-Promoting Properties of Short-Chain Fructo-Oligosaccharides. Nutr Rev. 2002;60(10 Pt 1):326-34.
Buddington RK, Kelly-Quagliana K, Buddington KK, et al. Non-Digestible Oligosaccharides and Defense Functions: Lessons Learned From Animal Models. Br J Nutr. 2002;87 (Suppl 2):S231-9.
Dai D, Nanthkumar NN, Newburg DS, et al. Role of Oligosaccharides and Glycoconjugates in Intestinal Host Defense. J Pediatr Gastroenterol Nutr 2000;30(Suppl 2):S23-33.
Roberfroid M, Slavin J. Nondigestible Oligosaccharides." Crit Rev Food Sci Nutr 2000;40(6): 461-80.
Sat G, Keles F. The Effect of Soaking and Cooking on the Oligosaccharide Content of Seker a Dry Bean Variety (P. vulgaris, L) Grown in Turkey. Pakistan Journal of Nutrition. 2002;1(5):206-208.