If you do, then I guess we've pretty much covered all the bases here. I strongly disagree and believe that these are legitimate wartime targets.
However, if I have misunderstood you and you don't agree that these are protected targets, then at what level does it become a war crime and what level is a purely legal and military strike against national assets?
Surely, though, you're well-read enough to know that both Hiroshima and Nagasaki were centers of communication, supply, and command and control for numerous military field forces and naval units. I'm sure that you also know that the Japanese factory system relied on a multitude of small, widely scattered but numerous, family-level assembly points and factories, all contained within populated areas and lending themselves immune from any type of precision targeting.
Finally, even the present Geneva Convention recognizes that tactical and strategic targeting of civilians is sometimes unavoidable ...
4th Geneva Convention Relative to the Protection of Civilian Persons in Time of War, Part 3, Article 1, Section 28:
"The presence of a protected person (aka civilian noncombatant) may not be used to render certain points or areas immune from military operations."