To be perfectly honest, I have no idea what boot you're talking about. I thought Honda only sold complete ball joints, complete with their "boot," only in certain cases though.

Also, it is possible for a CV joint to go bad with the original boot intact. I have seen boots leak grease with the boot in place and in good condition, and if they loose grease, they can die while still looking perfectly fine. Is is uncommen, but it can happen. Don't argue with a ticking CV joint.