It's pretty easy for a drone to fly higher than almost all the obstacles you just listed. Skyscrapers and smokestacks are going to be a concern, but those don't move and it's easy to do offline route planning to avoid those. Construction cranes and other temporary obstacles are a problem, but some rudimentary sensing and fallback to human control should solve that.

As someone who makes delivery robots for hospitals, let me say that I envy navigation problems of flying drones. I'd seriously worry about power and range and weather and how you recover a drone that has a problem and crashes, but not navigation in general.