Rabizo, I changed some parameters in my mission and played again.
I can confirm that (in this particular mission) B5N2s are dropping torpedoes from altitudes higher than it is written in the *.mis file. But it can be managed a bit by creating more waypoints and making the approach route more "shallow". Still, they drop higher, a minimum of 70 m or so, instead of 30 m.
Flying boats, surprisingly, go for another extreme. They fly lower than "ordered" and drop lower. Sometimes, if the "fragile torpedoes" difficulty switch is enabled, it can lead to the torpedo not working, since the drop was at 20 m instead of 30 m (for the Type 91 early). And that brings me to another question, at least to myself: why should I keep "fragile torpedoes" on and waste my time trying to "teach" AI again and again...
So, I choose to set the "fragile torpedoes" OFF in my mission-making. But it's just me.