Those need to be completely ground out and the plates re-prepped. I wouldn't weld completely around the plate. Instead I would stitch weld each plate. Weld the corners and in between the welds but not the whole plate. A long, continuous weld will build up too much heat in the frame and may cause it to be brittle. If you want to seal it, use RTV or silicon after it is cooled on the open areas. BTW, you will be hard pressed to completely seal out rust even doing that and painting. Both the slider plate and frame at and around the welding area needs to be bare metal in order for a proper weld.
If your "welder" is using MIG, it needs to be done inside, with no wind or breeze that can blow the gas from the weld, which could also cause the holes you see.
If your welder can't do it right, you need to find another shop that can. Improper welding can screw up your frame and cause serious damage to your vehicle or others around you.