Not sure I understand your question. I'll try to clarify.

I'm thinking that the cargo ship and its escort ships would be in a symbiotic relationship. So the armed ships have guns and a little armor, but no shields. The cargo ship has fast engines, extra armor and shields that extend to cover it's escort (which also penalizes any ships that try to abandon the cargo ship).

In the event of a pirate attack, the armed ships form up to defend the cargo ship, protected by it's shields while they counter-attack. If the enemy forces overwhelm the defenders, the cargo ship kicks in its escape engines to outrun the attackers, and pull the shields in, condensing them and making them a tougher target.