Why does API 653 prohibit lap patches on shells >1/2" thickness.

I think it is becasue if your large, expensive, high capacity vessel has a hole in it the enigneers who wrote API 653 think should put a butt-welded patch in it and not fool around with lap patches that have a low joint efficiency as well as load path and/or other issues. Trying to guess why a standard is written is a tough path to go down.
The cost savings is simply not worth the risk. If you don't follow API 653 and there is a failure you and your boss can have fun standing in front of the judge and tell them why you chose not to follow the standard but instead save some money while endangering the environment and surrounding comunity.