By the looks of it there's a step in the outer sill where it meets the inner sill, creating a slot.
The biggest issue is condensation forming rather than rainwater or whatever getting in so anything to allow airflow will help no end, even if just making sure that the inner sill is vented to the car interior will help.
The trouble with simply drilling holes in the underside of the outer sill is that the rust has a nice fresh bare piece of metal to start eating at! Even if paint is dabbed on.