contains spoilers from Reloaded and the Animatrix
In the Animatrix it is shown that the first things similar to hovercrafts are built by Zero-One Heavy Industry Corporation, combining "a helipod" with an "air-jet".
Later in Reloaded, Neo talks about the Architect briefly about the future of Zion.
By that point the events already undergone would mean Neo was proposed to a difficult task which he would need more ships than those then available.
But if you check the nameplate of Neo's ship, it says:
Mark III No 11. Made in the usa - Year 2069.
But Neo would most likely not be able to build such a ship in the USA in 2069. The ship is worn. It's not just out of the factories. It is more like a replica of an ol' matey...
How is Neo supposed to get old ships? How are they found in this condition?
If it's the machine storing these ships (because it is definietly not Zion), then why are they not using them for the war, or to build better squiddies? They would have the time to study the ship however they want.