Unless you are going put your car back on the factory jig to weld the chassis together then they serve no purpose, so weld away. Most people think they are drain holes from the priming stage of painting but that's not there primary reason to exist, back in the days before computer positing and welders the big holes had a pin that located the hole and a locking pin was installed to hold the floor flat and the smaller 1/2 dollar hole locked it straight.