You're right, they can have trouble with it in real life. I'm weird that way too. I'll get the humour or sarcasm, metaphor, turn of phrase, whatever straight away and a few seconds later my mind starts thinking about what I woulda heard if I HAD taken it literally! Maybe I have half the disorder, I dunno!
As for not getting it when reading, I dunno, could be a problem with your attention span or reading speed. Or maybe everyone has the same problem. Online it's difficult cos you can't convey tone, that's a main cause of flame wars- someone says something that gets taken the wrong way and on it goes.
What kinda stuff are you missing?