They mean the same thing, really. The difference has little to do with grammar. English grammar books never explain this. Grammar books will never help you to decide which way to say it. Shame, because the difference is real and it is important. The difference is imagery. Present participles paint mental pictures. They DESCRIBE. For that reason, they can be more emotive. The simple present and past merely state FACTS. With this in mind, I suggest that... ...you use the present participle if you are talking to your child or someone you care about. It works better when you are concerned. Use the participle in conversation with a friend. It is easy going and less direct. "Has your throat been hurting?" is as much a question as it is an invitation to start talking. Use the participle when you don't mind hearing a long answer. Use the simple past "has it hurt less?" if you are the doctor. You just need to get the facts. Say it when you don't want to hear a long answer. Those are just suggestions. You will sometimes want to do the opposite. A mother talking to her child might just want to get the facts. The doctor might want to make the patient feel relaxed.

Both questions are grammatically correct, but they have slightly different nuances: "Has your throat been hurting less since then?" - This question implies a continuous or ongoing action. It suggests that the condition of the throat hurting less has been happening over a period of time leading up to the present moment. "Has your throat hurt less since then?" - This question focuses on the state of the throat hurting less at specific points in time, without necessarily implying a continuous or ongoing action. It suggests a more general inquiry about the reduction in throat pain without specifying the duration or continuity of the improvement. So, the choice between the two questions depends on whether you want to emphasize the ongoing nature of the improvement (Option 1) or simply inquire about the overall reduction in throat pain (Option 2).

Both are fine. When speaking of a particular time (now, then, since then), hurt can be either simple or continuous with no change in meaning. My head hurts = My head is hurting. My head has hurt for hours = My head has been hurting for hours.