Ships that can fly have been present in a variety of stories throughout history, but also exist in a few times and places. Due to the many sacrifices needed to make them work however, including cost, limited cargo and especially vulnerability, they are quite limited in use. An old saying states than any dragon could take down a fleet of flying ships, declaring them useless in war as such.
Two places unusual for their use of flying ships are Philosophia (inside the Dragontears) and Canath around the Celestarian Sea. Both are used to reach floating islands, such as Backbreaker Island and the Eyne respectively - though in Philosophia they’re also important to navigate enormous architecture.
The sea-bound ships of Celene, capable of mounting heavier Copper Cannons, are built to be able to shoot down hostile flying ships at low altitudes.
Flying pirates are a common feature of pirate stories. They have existed on at least some occasions throughout history, using their fear and surprise factor to their advantage.
Certain explorers have also made use of flying ships, though this requires large up-front investment.