cowl rust problems.

I tried to take pics today but camera went haywire. My question is would there be any bad effects if I were to weld closed the fresh air intake. I am talking about the grated area at the base of the windshield. I was in there today and there is nothing left to the pan that collects the water. There are even some pinholes up by where the windshield wiper motor mounts. The first 18" on either end are completely gone.