I've just noticed recently troops disappearing after all 10 are running to the maproom cause the C-47 on the ground was killed. That's hogwash!
You are correct -- your statement is hogwash. Troops will keep running as long as the killed pilot does not re-up an aircraft or GV. Same with bombs -- they will continue to fall unless the pilot re-ups.
This is to prevent the gamey practice often used before of incessantly upping LVTs and dropping troops in dry-spawn islands, or upping PTs at spawns, and launching dozens if not hundreds of torps in quick succession at a passing task force. You can still launch your torps and let them run, but if you re-up to do it again, the original salvo disappears.
Had you paid any attention to the readme files about 8 patches ago, you would know this.