Single player mods? for which game and what is your definition of "mod"?
For SFC3, Generations at War and Dominion Wars come off the top of my head, they have single player conquest (GAW adds the non-playable tholians and DomWars adds five non-playable races in addition to the four playable) and lots of ships
But why limit yourself to pre-assembled mods? You can add as many ships you want in whatever capacity you want (playable, AI only).
Be creative and tailor you own SFC experience