Yeah, I agree with Charlie. For 'does it hurt much,' I would imagine someone asking this about a more minor injury or after a period of time during which the injury was in the process of healing. Like if someone had knee surgery and you went to visit them, you could say 'does it hurt much.' Or for a sprained ankle or something minor more immediately after the accident.
'Are you in a lot of pain' I would most associate that question with someone who is terminally ill, dying of cancer, etc. Although anything very painful like a bad back injury as well. To some degree it depends on context because if the person was obviously in agony and writhing in pain, it would be almost rude to ask them about their obvious excruciating pain. In that case, it'd be more appropriate to comfort them, tell them to breathe, tell them it'll be OK, etc.