As one may have noticed while considering the bombings in '44 and '45 on the main islands, whatever was bombed was often rebuilt in place after the war. If it was an oil refinery, an oil refinery was rebuilt; if it was an aluminum plant, an aluminum plant was rebuilt. Here is a list of the major aluminum companies in Japan today; a quick glance at the list will show that their main offices tend to be in Tokyo, Osaka, and...Shimizu. Plus ça change, plus c'est la même chose
So what did the Japanese do with military plants? Just retool them for civilian purposes?