New decking over old joists
There are some very interesting invisible fastener systems, often used for Ipe decking, that use clips fastened to the decking. These would screw into the joists, and would probably not line up with any of the nail holes. By the way, I would stay away from PT decking, that stuff is notorious for splintering, and I don't trust the chemicals in there for bare feet. There are some naturally rot resistant woods for decking, Ipe and redwood come to mind. I have heard mixed reviews about the plastic/wood decking, i.e. Trex, perhaps others have used the product and know more about it.