I would hope people would be wanting to do a 6-year program because they love research and want to pursue a career in academic ortho. That's why I want to do one.
If you're productive with your year of research, I can't see this type of a program hurting you for fellowship applications. If you were to get nothing to show for it (presentation, abstract, publication, grant support, etc.), I would assume it could hurt you. The same goes for taking a year off during med school for research, or completing a MD/PhD program.