The Matrix Wiki lists 11 ships being known in the Matrix Reloaded, and claims there are 12 ships in the Zion Fleet.
Given that they lose 5-6 ships when <PERSON> prematurely fires the EMP and they don't appear to have any in reserve, and General <PERSON> really laments having to lose not one but two ships to search for <PERSON> (1/6th of his fleet!), I am thinking they really do only have 12 or so before the Battle of Zion. If it has really been something like 50, where were they during the battle, and why was <PERSON> so sour on losing such a small number of ships relative to his fleet size?
You can see MARK and No. on some of the ships cores in the movies.
The Osiris, which is the ship that warns <PERSON> of the Machine army and subsequently gets destroyed has a nameplate on the core which says:
MARK VI No. 16
The Logos has the following core plate
MARK XIV Number 14
The Mjolnir has a core plate reading of
MARK XIV No. 62
Made in the USA Year 2111
Which is confusing, since it is listed as the largest ship in the fleet, and the Logos is listed as the smallest, and yet, supposedly they come from the same series. Also, since the USA hadn't existed for at least 6 generations of the Matrix, where was it really made?
The Vigilant core plate
MARK XII No. 32
The Nebuchadnezzar core plate
MARK III No. 11
made in the USA year 2069
Contrast that to the Pequod
MARK III No. 9
MADE IN THE USA YEAR 2026
It is listed as small, as opposed the large Nebuchadnezzar. 126
Also there was a 43 year gap from No. 9 til No. 11. They must take a long time to build.
At one time or another someone has created at least 11 Mark IIIs, 16 Mark VIs, 32 MARK XIIs, and 62 MARK XIVs. That is 121 ships. However, we know sometimes (or often) ships get destroyed by sentinels. It probably took them awhile to develop the early warning systems and EMPs that allow them to operate near the surface.
It could also be argued that they are salvaging cores and other things from long past hovercraft. That would explain the random dates and MARK series on them. If they were just scrounging up a power core, and decided to build small ship around one and a large ship around another, it could explain some of the discrepancies.
Apparently all of the MARK series are ascribed to verses in the Bible. 126