No one can really know if anyone is truly AFK. But the best clues are to be had by the people running the servers.
I am not saying everything is perfect, and I am not saying anything needs fixed, and I am not complaining about anything, but here are some ideas to ponder (or ignore if they cause you issues cause I am not even advocating them):
…If input (clicks) is not received from the pilot to the server in a certain time frame (say ten minutes) all ship modules turn off including the cloaking device
…and/or only the cloaking device shuts off
…and/or he ship begins to flip flop aimlessly in space (indicating the pilot is not conscious enough to control the ship) (ship control is meant to be direct mind control after all isn’t it?)
…and/or the ship begins warping and jumping to the nearest friendly or neutral station (could be said to be a safety feature as the ship thinks its pilot is dead or about to die)
…or the ship won’t try to jump if no friendly or neutral stations but instead warps to the nearest temperate planet or moon or next best thing if none in system.
…or the ship will just go to the nearest station and attempt to dock, even if unfriendly.
…or the ship will stop everything its doing and immediately go into safe log off mode and be gone in 30 seconds.