Perhaps (although maybe this was obvious) differentiate them in the same pattern as the races are differentiated?
i.e. Assuming your Orcs and Humans are done like Blizzard (Orcs = emphasis on melee & brute force & large groups, // Humans = emphasis on ranged/melee mix, tactics, utility), you can make the ships like that too. (Orcs have lots of smaller, cheaper, rickety-er ships with crude weaponry, along with some huge Juggernauts; Humans have smaller groups of more expensive, but more tactical ships, as well as advanced weaponry on their 'battleships')