Each has merits, but in our evaluation, if you are able to overcome the aircraft design challenges, fixed-wing offers a far more capable platform. The stratosphere has winds that can exceed 100km/h. With balloons, station-keeping is an enormous challenge. We spoke to a lot of people in the Google Loon project, and ultimately this became a defining problem for them. Airships/dirigibles help a bit, but still have to drift in strong winds - beyond that, they also become extremely large and expensive to work with.

Probably for control reasons. You can send balloons up to that altitude, but they'll go where the wind takes them.

I'd guess because it's less prone to get interfered with by wind, more easily controllable, and can stay up longer if battery power lasts overnight.

I too would like to see more autonomous hydrogen balloons flying. Even on tethers to get height cheaper than a tower.