I went and made more comprehensive tests and actually the manual and deano are partially right.
That above 1000 meters brain loss happens only over large land mass, over the sea the planes fly happily no matter what the height is, although they can
sometimes get confused there as well but this happened only with extensive timeacc use..
I would need to do some longer testing sessions but it
seems like height and waypoint distance is some kind of factor, lowering a plane (over land mass) flying at 4000 meters to 3000 meters made it find it's waypoints easier although it did fly in completely erratic paths.
But then again, it's impossible to have conclusive results because the AI may not approach things the same way twice in a row..
So it's better to say that yes, try to avoid over 1000 meters when using AI planes..
But, nothing suggests that triggers won't detect planes flying that high. Setpossed a plane into a trigger area at 100000 meters height and it got detected.