The penalty for targetting something faster than your tracking speed is only calculated once. With a turret involved it would be the worse of the fire control tracking speed, or the turret tracking speed. The only time that having a turret tracking speed greater than your fire control tracking speed is when you go to upgrade a ships fire control. For point defense if you only have to upgrade the fire control to take advantage of the new tracking speed it can be a fairly simple upgrade. If you also have to replace the turrets involved the cost often can become quite significant. When you design a turret, check to see if the hull size penalty for a higher tracking speed is significant. For many point defense aplications you can get most of the tracking speed for the next fire control upgrade without it costing to much. This is only a significant factor for ships you plan to upgrade, but it can make a difference.
brian