Subsystems aren't supported well in FS2 at all, except for engines. Disabling weapons doesn't slow down rates of fire for turrets, and is impossible to destroy on fighters without taking the craft with it. Disabling comm on capital ships doesn't prevent those ships from transmitting messages, and taking out sensors doesn't reduce acuracy. But theoretically, destruction of the bridge should lead to a more erratic AI, or possibly complete shutdown of the ship; disabling comm should prevent the transmission or reception of any messages by the target ship, including the ability to call in reinforcements; destroying weapons should reduce the available power to ship weapons systems, slowing turrets and missile launches and disabling beams alltogeather; taking out sensors (or your CIC) should reduce the accuracy of all ship-based weapons and possible cause the ship to stop manuvers/manuver based on last known position of enemy ship (and possibly collide with nearby objects); disabling navigation would prevent subspace jumps, and so on.
