Every NASA crewed launch to ISS from US soil is on a stack that uses Linux for avionics: Falcon 9 and Dragon 2. The Starlink constellation is also a massive deployment of Linux nodes in space.
The backup NASA commercial crew system from the 737 Max people hasn’t flown people yet and probably won’t this year, perhaps never. They somehow managed to have two critical software failures on their first orbital flight test, either of which would have caused loss of vehicle without intervention. Both should have been caught with comprehensive testing.