After the humans discovered the machine army digging toward Zion, Commander Lock recalled all hoverships in preparation for the Battle of Zion. Lock believed he needed "every ship" for the defense of Zion:
Lock: I believe I need every ship we have if we're going to survive this attack!
Councillor Hamann: I understand that, Commander.
Lock: Then why did you allow the Nebuchadnezzar to leave?
Councillor Hamann: Because I believe our survival depends on more than how many ships we have.
So how many hoverships did Zion have? I am interested in how many hoverships were used by the Zionists during the events of the films, up until the Battle of Zion (after which there were obviously a lot fewer of them still operational).
The Matrix Wiki has a list of known hovercraft which provides a rough lower bound on the number of hoverships available. However, many of these are from The Matrix Online (which occurs after the Battle of Zion); some of those ships may have existed before the Battle of Zion, but some of the them were salvaged from hoverships destroyed before or during the Battle of Zion (such as the Logos II, which was salvaged from the Logos).
The answer would probably be found in a remark from any canon source (or from the Wachowskis) of the nature "Zion has 50 hoverships". Also, a remark on the number of hovership captains is acceptable since there is one captain per ship.