Yes, overpenetration is a concern. When NYPD switched over to 9mm semi-autos they issued FMJ. They ended up switching to JHP because they had several instances of FMJ rounds not only exiting bad guys, but continuing on and injuring bystanders and other officers.
As others have stated, there are other reasons to stick with JHP for self-defense use. 9mm FMJ makes narrow wound tracks that can "self-seal" to a certain extent because the elastic nature of tissue causes it to stretch before being penetrated, then springs back closed, minimizing trauma. Modern JHP do a good job of both penetrating and expanding, with some bullets recovered from actual shootings often looking like the expanded bullets from gel tests and marketing ads. The result is increased tissue trauma. And if they don't expand, the edge around the hollow cavity has a higher likelihood of causing trauma than FMJ due to a cookie-cutter effect. More trauma generally means better effectiveness in stopping an attacker.
JHP bullets also seem to have less ricochet potential. While this is often considered a benefit for misses or through-and-through shots, it can also improve effectiveness when bone is struck. Unless it hits the bone squarely, FMJ can ricochet off the bone and may not cause as much damage as a JHP whose edge can "bite" into the bone and damage it.
Have their been success with FMJ and failures with JHP? Sure. But I'd much rather have a round that gives me better odds of stopping an attacker.
JHP are not "magic" bullets. Don't count on "one-shot stops." A lot of variables are involved, such as the attacker's mental state, physiological state, physical build, drug use, etc. The only variables I can control are how well I can shoot and what type of ammo I use. I'll stick with JHP because they improve the odds of stopping an attacker, as well as reducing the odds of overpenetration.
Also, I've never understood the reasoning behind the "misses are more of an issue than overpenetration." Well, duh! How does that mean it's not a good idea to use JHP? I've never heard of anyone shooting well with FMJ ammo and then all of a sudden can't hit what they're aiming for with JHP. That's the only situation where that argument makes sense.
This is just my opinion. I'm sure plenty will disagree. Do your own research and come up with your own conclusions. However, I think you'll find that data supporting JHP as the best choice for a self-defense load.