Besides historic accuracy, any reason not to weld the U-shaped holes in the passenger floor?

I don’t know what the reason for the holes but I’d use silicone, sealer to seal that to keep water out and it’s still removable in case someone want original.

The factory sealed those up with a metal disk stuck down with caulk or seam sealer on the interior side of the floor. They might have provided drainage during manufacture but they don't serve any purpose now.