In the second movie of the Matrix Trilogy Commander Lock says to Councillor Hamann:
I believe I need every ship we have if we're going to survive this attack.
But in the third movie none of the ships are used for the final battle except the EMP from the one which Niobe flies into Zion. And even that EMP is under Lock's view a mistake.
So, for what does he need all those ships?
Lock insisted that all the hoverships be used for the Battle of Zion so he could use their EMPs and guns. The reason the hoverships did not appear during the Battle of Zion in the third movie is that most of them were destroyed (off-screen) at the end of the second movie:
Roland: Lock was right. He guessed that the machines would cut off the mainlines in and out of Zion. He thought a counterattack might surprise them. It sounded good, we figured we had a shot, until someone screwed it up.
Colt: An EMP was triggered before we could get in position.
Mauser: 5 ships were instantly down.
Colt: When the machines broke through, it wasn’t a battle, it was a slaughter.
The Matrix Reloaded (transcript)
Aside from a few ships operating in or near the Matrix at the time for various reasons (e.g. the Nebuchadnezzar) most of the hoverships were destroyed prior to the sentinels' breakthrough in the Zion Dock in the third movie. Lock did use them for the Battle of Zion, we just didn't see them.
Lock thought Niobe's use of the EMP in the Zion Dock was a mistake because she used it in the Dock and in doing so disabled many of Zion's defenses:
Lock: That's the problem with you people. You can’t think for five minutes in front of your face. That EMP knocked out almost every piece of hardware and every APU. If I were the machines, I would send every Sentinel I had here right now. Saved the dock, captain? You’ve just handed it to them on a silver platter.
The Matrix Revolutions (transcript)
A better use of the hoverships' EMPs would have been far enough outside the Dock that the EMPs wouldn't disable any of Zion's defenses (i.e. before the machines broke into the Dock). That's exactly what Lock tried to do with his "counterattack", except that someone screwed up the attack and triggered the EMP too early.
