Generally, the reason I've seen given for cooking grains -- or rather, soaking before eating -- is due to the presence of "antinutrients" that soaking mitigates. I don't necessarily subscribe to this view, but do know people who soak their oats before any use, such as in shakes, because of it. Here's a link to weston price (which I'm not a fan of) describing this in more detail, and I'll include a quote (again, I don't subscribe to this view, but at least it's a rational explanation):
Be Kind to Your Grains
Be Kind to Your Grains
Grains require careful preparation because they contain a number of antinutrients that can cause serious health problems. Phytic acid, for example, is an organic acid in which phosphorus is bound. It is mostly found in the bran or outer hull of seeds. Untreated phytic acid can combine with calcium, magnesium, copper, iron and especially zinc in the intestinal tract and block their absorption. This is why a diet high in improperly prepared whole grains may lead to serious mineral deficiencies and bone loss. The modern misguided practice of consuming large amounts of unprocessed bran often improves colon transit time at first but may lead to irritable bowel syndrome and, in the long term, many other adverse effects.
Other antinutrients in whole grains include enzyme inhibitors which can inhibit digestion and put stress on the pancreas; irritating tannins; complex sugars which the body cannot break down; and gluten and related hard-to-digest proteins which may cause allergies, digestive disorders and even mental illness.