I can not remember that this was in HW1 and Cata. I remember that i finished Homeworld with a giant fleet i build up during previous missions that overrun the enemy positions without a problem, this game was more difficult at the beginning of the campaign where do you not have enough resources in a mission area to build many ships.
But in Homeworld 2 i was overrun by superior forces right in the second mission after i take time to build up a fleet in the first.
And in Cata i only remember this in one mission, because it was a story requirement. It was the mission where the Beast awakes, if you have a lot of ships around it, the beast will overtake them completely and the mission will be a hell lot harder. But later it was only more difficult if you are losing to much ships to the beast, of course. But as far as i remember, the strenght of the enemy at the start of the mission was always the same, regardless how many ships you have.