As a historical curiosity, this dilemma actually kind of really happened when airplanes were invented: could landowners forbid airplanes from flying over their land, or was the ownership of the land limited to some specific height, above which the landowners had no control?

I think a similar issue arose with satellites and whether you need a country's permission to fly over it. As best I can remember Glenn Reynolds wrote about this, but I don't have a cite. Also, you might want to look at property law where there are always questions of how far property rights extend and what constitutes unlawful interference with property rights.