I've been intrigued by this problem for years and surprised plant breeders haven't come up with an answer.
The main reason the pods are empty is because the flowers weren't pollinated, but that doesn't explain why you often find a small pod packed with beans, and a huge pod which has only one or two seeds, on the same plant.
I think the black marks are merely damage from insects like black fly which cause the empty pods to rot. Deformed pods are quite common too in my experience.
Having a good variety helps a bit, and the green longpod types are usually better I find.
But like you I'm surprised at how difficult it is to get a bumper crop on a few plants compared to the ease with which other legumes, like French beans, grow.
If someone could develop the 'perfect' broad bean they'd make a fortune.

Thank you Bertie, a very comprehensive answer.