I'm wondering the same thing as you. I did my PhD work in orthopedics and genuinely want an academic career. However, considering that only about 10 to 15 of the 800+ applicants are MD/PhD students, this may help or hurt. I think orthopedics is still one of those traditional surgical fields that is predominantly looking for the best clinicians possible hence those who have the best grades and board scores. To be honest, I think the vast majority of training programs could care less about research and doctoral academic training. The problem with doing an MD/PhD is once you come back to your third year it is common knowledge that the delay in clinical training hinders grades but not clinical performance. There was recent study which showed that people who take more than two years off are much more likely to do worse on shelf exams than their competitors who have just taken their boards. Several other traditionally competitive fields such as Optho, ENT, derm, Rad Onc have recognized this trend but still recruit heavily among potential physician scientists. In fact, in these fields MD/PhD applicants tend to match at the nation's best programs. This is not often true in orthopedics. If you compare the advancements in these fields over the last 50 years with those in orthopedics you will see that ortho has not changed much.
In fact i know one MD/PhD applicant who was on the interview trail a few years ago. He had to "justify" completing a PhD in many of his interviews. He told me that the degree actually worked against him. Some interviewers saw this as an extraneous glorified hobby and a distraction clinical training. But this just one (N=1) person's experience, so you cant make too many conclusions.
This is a bit of a tragedy since orthopedic research is one of the most poorly funded areas of in all of biomedicine. Almost every person you meet will have some type of orthopedic pathology in their lifetimes. There is a lot of work that needs to be done but very few people to do it. I would suggest that you go through med school get honors in all your clerkships, rock your boards, and match in orthopedics. Dont get a PhD hoping to have it help you match. Do research if you are truly interested in scientific inquiry. If not, try international medicine. Help out some kids in a foreign country. These things will stand out much more than research experience.