It depends what you mean by "a very long time", but the idea that stars are like the Sun has only been around for about 350 years, and only generally accepted for about 200.
People didn't know about air until the 18th century, and so the idea that you might not be able to breathe in space came later than that.
Okay. So what? What does air in space have to do with there being stars? Hell, what does knowing that the sun is just a star have to do with knowing there are stars?
The medieval Arabic astronomers who named a huge chunk of the stars named before the 18th century knew that stars were objects separate from the Earth, that moved around outside the Earth, and weren’t like, holes in a dome above the Earth or whatever.
There is a story, I believe Chinese in origin, one of the oldest written stories, about someone traveling to the moon in a vehicle.
Space Opera does not require science. It requires space, stars, the ability to navigate by and to stars, etc. It doesn’t require not being able to breath in space.
Who is familiar with which tropes depends on what group of people you are talking about. People who like steampunk are familiar with steampunk tropes. "Aether" was only science for a relatively short period of time, as evidence mounted that Newton was wrong about light and Huygens was right. Everyone knows waves require a medium to propagate, right?
Completely irrelevant. What matters is that it’s an idea with traction amongst people who know anything about steampunk and things related to it.
The advantage of "Astral" was it was popularised by the 1960s counterculture, and was never science. Since it was never science, it is not subject to being disproved, and therefore can never replaced by something else.
Being disproven is irrelevant to any of this. It isn’t science fiction, it’s fantasy.
People didn’t bounce off Spelljammer because the phlogiston is old disproven science. They bounced off it, in part, because the phlogiston is a weird, unfamiliar, and fairly hokey, idea that has absolutely nothing to do with being able to leave a home world in a ship and navigate to a distant star and then physically travel there. They bounced off it because it insisted on using the basic ideas of D&D cosmology like the crystal spheres instead of letting worlds just be physical objects in a vast expanse.
Beinf able to breath in space or not doesn’t matter
at all. It’s purely a choice to make based on aesthetic and what things you want to be possible without special equipment. In my game setting I chose to have a special gas that seems to collect around stars and other large gravity wells, and know one knows yet how it’s generated, that can be used to power magitech devices like “Aether ships”, and can be breathed by nearly all life forms because it’s magic gas. Because that made some fun stuff possible in the setting, and fit the aesthetic I wanted, of a galaxy somewhere between steampunk and Flash Gordon, with elements of Star Wars and Treasure Planet and Final Fantasy.
And it works because all of it is either familiar or easy to grok and
use in play for most nerds and even a lot of people who aren’t especially nerdy, not because it avoids disproven science.