Sometimes if a weld approaches a fillet weld, we are required to spot face the surface of the hole that ends up near a fillet weld to provide a flat seat for the fastener washer, nut, or bolt head. Sometimes this spotface cuts into the fillet weld. I have seen where some full pen. welds have been drilled through after surface milling operations. Obviously, if a bolted connection happens over a butt seam, one would think that the butt weld would have to be machined, milled, or ground flush to provide proper bearing for the mating parts. It would be hard to layout acurately and drill a hole if the weld was not ground flush.
I do not know of any code restriction prohibiting locating a thru hole over a butt weld, I do not think it is a common engineering practice though. You might have some problem tapping such a hole in some materials if there are some harder to softer heat effect zone issues.