OurGangsDarkOath is right about how the number of ship types increased and they added upgrades further increasing ship options but neglected to increase the number of slots to give players a better opportunity to sail a wider variety of available ship types.
Yes, Disney got very lazy with POTCO after a while and actually fired most of the coders, leading to questionable options in the game.
At least 6 slots seems a reasonable request, given the amount of ship options available, for both plundering and SVS.