I feel like it should focus on taking out enemy cargo instead of lowering it's health, that way the damage you take is less.
Cargo is health, unless I am not understanding. Regular (white) dice and cargo (orange) are all counted towards hitpoints/health. The enemy gets to decide where to take damage, just like you, as the player, does. I would rather take a hit of 3 damage on a 5 die than completely lose a 1,2 or 3 dice. The enemy does the same. The more dice you have, the better your damage output is with more potential scoring dice.
Sometimes cargo is not good. If you run into a pirate ship with an unwanted potential crew member and refuse the deal, the pirate will go ahead and fight you. If you only have a 2 points of cargo, usually it will be worth it, but if you have 20 points of cargo for a 'mediocre' crew member, they will force you to fight. Depending one where that happens in the run, it can be bad.
Mates are maybe the best early game crew as you will get more encounters. So many other super great combos of crew are available, though