I think DS-9 is an exception that should be ignored. In all the rest of Trek it's implied that ships are in short supply and each one is precious. In ST1 the Enterprise is rushed out of construction to meet the Vgr threat solo. In TNG only 39 ships are available to intercept the Borg cube with Picard aboard.
It's only in DS-9ís Dominion War we start hearing about hundreds and perhaps thousands of ships. My thought is the writers got carried away with hyperbole and wanted to make the battles sound epic. They didn't sit back and realize how they screwed up Trek canon and how it doesnít fit in with the rest of the Trek universe.