Some/all of that have less to do with war and more to do with general disaster preparedness.
* Bomb shelters provide shelter from...bombs, yeah
* Windowless hallways provide shelter from tornadoes (no glass to break/become shrapnel)
* The heavy metal doors are firewalls that automatically close when the alarm goes off (most are hollow, won't do shit against assault weapons and predate even Columbine)
I suppose you could put windows between the classrooms and hallways, but those have their own associated problems to overcome: increased noise, more windows for students to break, safety in emergency situations, etc.
As for non-connected classrooms, where you need to walk outside to go between rooms, I've always thought that was to solve the same problems. Cheaper to build/renovate/modify/expand, easier to clean, less noise and fewer students running into each other.