Now, I am trying to incorporate these flying ships into a setting similar to early 1800's Europe, around the time of the Napoleonic Wars, save that magic exists, similar to that depicted in Ars Magica 5 (warning: 20Mb PDF) save that magi operate openly, and are active at all levels of society.
The TL:DR of Ars Magica is effectively that magi can accomplish many things on a small scale over a limited timeframe, but large scale, long timeframe stuff gets difficult and expensive, and Magi comprise around only 0.05% of the population. There are simply not enough of them to go around. Most combat ships might have one, a ship-of-the-line would have one or perhaps two, and a flagship would have two or perhaps three. Fortresses might have several. However, Magi would effectively cancel each-other out in broad terms.
However, it has been pointed out to me that the fact that has historically allowed an empire to form is the effectively two-dimensional nature of warfare: since troops may only move en-masse on the surface of the world, in order to reach the heart of an empire, you must first fight your way across its' breadth.
Even today, that is true; despite having troop carrying aircraft, troops may still only be delivered to a battlefield in large quantities by surface transport.
However, with the existence of sailing ships with a potential armament similar to a ship of the line such as the 1808 HMS Caledonia, or the potential to carry an equipped body of 300-400 troops (where the largest modern troop-carrying aircraft can carry only around 100 equipped troops) and the ability to fly as high as it is humanly possible for the crew and passengers to breathe and continue to operate the ship, this means that it ought to be relatively easy to overfly the outskirts of an empire and aim a decapitating strike directly at the enemy capitol.
Historically, ships of the line were prevented from becoming unstoppable mobile fortresses by the simple fact that they could only sail where there was sufficient water, and that their wooden construction prevented them from using the best defence against them, namely heated shot, and additionally, the stone construction of the shore fortifications would have made heated shot less effective.
However, where ships may fly above land or sea, and can have considerable advantage in altitude, and where heated shot falling back to earth would pose more risk to the possessions of those firing it, flying ships would become unstoppable except by other similar ships. In such a circumstance, nations could be expected to be small and numerous, as the only effective defenses could be applied to small, localised structures.
So, my question: given the aforementioned changes to the technology of age-of-sail warfare, namely keels allowing flying ships, and Magi, how could empires be established?
To be clear, I am not looking to change the way these ships work, I am looking for innovations - preferably mundane, but if necessary they could be magical - that will prevent the indiscriminate overflight of a nation's sovereign territory, without having to have defence in depth.
To put it another way, I would like a way for nations to be able to establish an effective defensive perimeter, rather than having to blanket their entire area with defences.
Since it would appear that some are not reading the linked articles, I'll restate here how the keels work:
In this universe, Ether Theory has been proved: Ether is a universal medium through which everything passes. Most substances barely interact with the ether, but some interact more strongly, and some interact differentially, having low resistance when moved in one direction, but high resistance when moved in another, like a pipe moved through water. The amount of resistance that an object provides to movement is dependent upon its volume. A couple of cubic metres of keel would be enough to support a flying ship massing up to four thousand tons so that it would descend at a rate of a few metres per minute if it was not moving.