No, bad idea, standing water is more of a rust trap then open sills, if condensation / leakage from the rain / etc can't get out then it's going to start rusting faster as it pools in your sills.
Chris
Where does the water get in if not via the sill vents though?
Yes, condensation, have you ever gotten into a car with the windows all fogged up?
Well the metal is the same way with a temperature difference inside and out the water will condense on the metal and drip.. More or less like sweat.
If you could build the car in a completely dry environment and seal the sills, the area at the base of the window posts, up in the cantrails, and everywhere else the box section is open to so it was an air tight void, then yes they could be sealed as there would be no way for moisture to get in there. But unfortunately it's not that perfect of a world.. and vents in doors and bodies etc are there to help prolong the life of our cars.
Instead of sealing them up, a better way would be a regular scheduled maintenence of checking to make sure all the drains are clear and free of mud or leaves or other gunk so the liquids could easily and quickly leave the area.
Chris