As I understand it, many of the plane crashes that occur in this region happen on flights taking tourists from Kathmandu who wish to trek to Everest base camp. The airport runway closest to the camp is very short and narrow, and has a significant uphill gradient, making landings extremely challenging for even the most experienced pilots.
The flights that are being discussed here are those which give passengers a view of the mountain and then return to Kathmandu which, as Di correctly points out, last about one hour and do not attempt the hazardous landing near to the base camp. But I guess even those flights could get into difficulty if weather conditions take a sudden turn for the worse. Of course if I did decide to visit Nepal then, like most people, I would love to take the opportunity to view Mt Everest on the one hour flight. It would seem such a shame not to try!
As for hot air balloon flights, despite the crash in Egypt a few years ago, I would have loved to have had the opportunity to take a flight recently in Bagan but unfortunately the schedule didn't really allow time. Incidentally, I've just read that dozens of tourists have been injured when balloons crashed at Cappadocia in Turkey.
So looking at al this from JY's perspective, I can understand that given today's 'compensation culture' they are reluctant to offer these opportunities, thrilling as they may be. That doesn't mean that they couldn't allow free time in the itinerary for these activities, and if people want to do them they could ensure that they are covered by their holiday insurance and undertake them at their own risk.
Mike