As the game progresses, the man from IGN will report numerous advances in space flight technology. From better shields to more powerful weapons, technology marches on. Supplying your ships with these upgrades can get costly, especially when equipping a large fleet. The solution is simple - don't do it. At least avoid upgrading all ships.
Pirates have a tendency to target the larger vessels that are carrying the more valuable cargo.
Spend money to give these platforms the latest in weapon technology and leave the older, smaller shuttles to their own devices. On the other hand, Glenn Oliver claims the amount of ransom the pirates demand depends on how easily they feel they may defeat the targeted ship in combat. In other words, Pirates will demand less ransom from merchants packing the latest in weapon technology than from cargo ships with last year's defense systems. Every ship in the fleet should be configured for every stop - no ifs, ands, or buts. Although at first glance this may seem like a daunting task, it isn't hard if you configure each ship when built.