I wouldn't weld the holes shut after bonding. You'll burn off the bonding adhesive near the welds, which will give off nasty fumes and reduce the amount of surface area you have bonded.
If you're that concerned about the screws, remove them and cover them with seam sealer, the panels will be plenty strong without them. Or just leave them in and knock the points off with a grinder so they don't catch you when you're working under the car.