I was trying to think of what was in DF that nobody seemed to have a topic about yet, and after searching for a hour I find no topics on this. Studies have shown that stress can effect natal development and is one of the probable causes of learning disabilities in RL. Why not have it in DF too? Stress such as too much physical exertion and traumatic events causes all sorts of problems (usually through a raise in cortisol in the brain) which then effects other chems (neurotransmitters) which in turn effect development.
Of course, it would be different for dwarves, as I feel that the stress from being away from work should be what causes problems, along with other things (goblin siege, starvation, elves in general, dehydration, lack of alcohol, etc.) I feel it would give yet another reason to keep your dwarves happy, because if you don't their kids will have problems. Still, that is not the only issue that could arise here. There is also the genetic qualities of learning disabilities, and how some are thought to be caused by genes (ADHD). I don't know whether or not dwarves would have the same LDs as us (dyslexia, autism, ADHD, etc), but I feel that there should be some representation.
And having these wouldn't have to be a bad thing, an autistic dwarf could be a savant in say, weapon smithing or something. Just that there would be things that dwarves with disabilities would be good at, along with things that they are not (trade possibility to learn cheese making for easily learning mining). Still if people don't like that idea, than maybe just have them have their stats tweaked slightly because of it.
Just a thought.