So, it seems the ship vs tower/castle debate never really took of.
Skyship :
+ More mobile, the lack of water resistance means that a skyship will probably have a higher speed than a regular ship
+ Probably better range in practice, if we intend to visit places like Lustria or Cathay, the higher speed and manoevrability of a sky ship make it envisageable.
+ Probably less threatning
- Less durable, whatever enchantements are put on, there is no getting over the fact that a ship made of wood is bound to be more fragile than a stone construction
Skytower :
+ More robust, with the possibility of using a dwarven fortress as a base we would be safer to engage major threats like greater deamons or armies
+ Higher carrying capacity, we could probably carry heavy loads such as multiple waystones, lots of supplies, a decent garrison, etc.
+ Probably more stable which might be useful in everyday life and for permanent installations such as observation posts, artillery stations, laboratories, storage, etc.
- Slower than the ship, although probably still pretty fast considering it can still fly without interruptions in straight line from point A to B
- Pretty intimidating, rulers might feel miffed when a flying fortress flies over their lands on the other hand, what are they going to do about it
All in all it seems to me that the main advantage of the ship is that we can go further, faster. However, I'd argue that the speed difference is mainly important outside the Old World. The combinaison of the gyrocopter and a flying tower already allows for relatively fast travel. I mean, even if the tower only goes a walking speed of 5 km/h, it's still 840km per week! Moving the tower from K8P to Laurelorm would be a few weeks at worst and if we need to go fast ourself we have the gyrocopter. On the other hand going to the ends off the world would probably be a journey of months with a flying tower.
The main advantage of the flying tower is it's staying power and carrying capacity. While the ship is also very potent, it still keeps a potential vulnerability to other flyers, artillery and probably battle magic, especially in prolonged engagements (although escaping such engagements is even easier for the ship than the tower). A flying dwarven fortification on the other hand... is something that feels like a strategic asset : be it reclaiming a nexus, helping out in a war, administrating territory, exploring hostile environements (ex : Chaos Wastes, Dark Lands, Forests, Mountains, etc.) or any other prolonged duty, I think a tower can do better than a ship.
TLDR : Basically I think the ship is better outside the Old World if we intend to explore while the tower is better to build on what we already accomplished inside the Old World with the factions we already interact with.