If the pin holes go all the way through and the back is exposed to the elements they should be filled. My concern with welding them is I don't know how many you have. Putting too much heat in a panel can create warping issues. I'm not familiar with all of the modern materials available but there may be some sort of an epoxy product that could seal the holes without re-welding. Again, if the holes are exposed to the elements on the inside (wheel well, fender, etc.) make sure both sides are filled to keep the rust monsters from inhabiting them.

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