Important Clarification: I have: Rules Cyclopedia, Poor wizard's Almanac II, Dawn of Emperors Gaz.
So I can't really appreciate the battle-readiness of the Alphatian fleet in something that I have never heard of, much less own.
However, from the Almanac the Alphatian flying navy seems very good, but nothing too awe-inspiring.
And the question remains:
Why would Thyatis consider to attack well defended independants halfway around the world, still loyal to Alphatia (that is Alatian isles). Yeah, Thyatis may decide to get a couple of these flying ships, but they could buy them instead of starting a war with something so far away.
I would really like to know why you think these flying ships were so important as I don't think that the benefit from having them would outweight the heavy losses and long war that Thyatis would get into in order to get Alatian isles.
As far as I have seen in the Almanac they are just that: Ships that fly rather quickly with 3rd-5th level crewmembers.