They were civilian centers with military factories and functions.
That is correct. All the Axis powers were willing to bomb the crap out of civilians working in those factories. No UN to bitch and complain about it.
This is where the concept of "Total War" comes in. Simply put, "Nobody is innocent, everything is a target because it adds to the enemy's war efforts.
BTW, Nagasaki was
NOT the primary target for Bock's Car.