From what I've seen it's related to ship size but mainly the amount of area triggers you use and how many get activated at once.
It seems once you get around 50-100 area triggers that are active you notice a huge FPS drop.
Decreasing the amount of "checks" per second will certainly improve performance but you might be able to fly through it without getting a signal then. So not sure if that is a good solution (the scaling problem won't be gone)