Not good to say the least, and unfortunately you absolutely must remove them and repair the area. If the shank of the nail passed clear through, meaning the hole has no taper to it, I'd grind the inside since you need to anyway for the proper patch, then carefully punch the nail back out from the bottom. On the outside I would use a small burr or stone in a drill/die grinder to clean out the hole and get to solid glass. Patch the inside, a bit of peanut butter on the outside. Cabosil could work, I prefer PB, longer fibers. I save the scraps when I do glass work for this purpose. You could also use an epoxy, then finish with gel coat and sand smooth.