Can I install insulation over the HVAC duct work and plywood?
You will not create a problem of moisture in or on the ductwork. The duct work is insulated to keep the condensate from forming on the outside of the pipes and dripping off from the temperature differences in the attic in the summertime with AC running. So more would help. What would be bad is if the duct work is flex duct and gets mashed under the weight of the added insulation on top of it. Don't underestimate what will happen once you cover it up and can't see have may have happened to it.

About the existing decking, I feel storage is valuable in any part of the home. To cover it up and lose what may be valuable space, at least in my mind seems a shame. But if you are not using it, and don't plan on it, then there really needs to be no concern.. If that is the case then insulation added anywhere in a continuous layer is a benefit. I would if it were me, pull it up and set 2X10 material on its edge and screw it to the joists so the new insulation could run tightly between the 2X material, then add plywood over that, ripping it 2 ft. wide if need be to get it through the access.