Yes, drill out the rivets. Coat the any exposed metal in the holes with some rust preventive paint, then either insert a plastic plug or something else to close off the holes. Those holes can be used for routing electrical, if needed. A grommet should be used to protect the wires from chaffing.
While you are playing with your floor consider painting front to back w POR 15 or similar. Up the sides a couple of inches. Tape off (do not paint) the the body attach bolts in case they need to be removed at a later date. Those can be coated with silicone or other protective paint that allows for future removal. All other through holes in the floor should be filled w plugs.
Pay attention to the body seams where they come together. Inspect for missing putty or skipped welds that create gaps for water and dust intrusion. A bright light under the van at night will show some of the gaps. Also look for telltale dust accumulation spots.
Lastly, IF you are putting down insulation and flooring, skip putting any sound deadening such as Noico on the floor itself. That is a complete waste of money, imo, and addition of useless weight. Put "some" adhesive sound deadener patches on the sides/top of wheel wells, up the firewall, inside face of the outer sheet metal on the walls and especially in the doors, where it helps deaden sound transmission.
Oh, and if attaching/fastening the wood floor to the van floor (unnecessary,with forethought, if you are installing cabinets attached to the walls and wood floor) , try to use the holes that are already present. These should be installed w rubber washers (and silicone) against the metal floor, top and bottom to reduce sound transmission through the bolts/screws and to seal off for water penetration.