Don't know why not. It is basically little different than broiling or grilling them other than the lower temp used. They should still get hot enough to blister I would think so you'll still be peeling them right?

Dave

This will be the first time for me to smoke peppers. I didn't know if they would char or not. The habaneros are so thin walled I didn't think I would be able to peel those. is it ok to not peel? I think some charred peel can add a good flavor.