Second question first, yes a hacker can just boot you if he hacks the system and kicks you out. The fiction in SR4a at the start of the unwired world section talks about exactly this happening. Once hacked a drone's node is the same as any other node. This is why the drone rules are in the unwired section rather than the vehicle rules section at the end of the combat section.
Ok first question now.
There aren't any really beyond being able to react to the situation faster. If you are on site with a drone and someone jams you, you have a better chance of dealing with it. You can take out the jammer or enable your own counter measures. At a longer range you just lose contact with your drone and need to find another way to it. Either situation has advantages and disadvantages tactically.
With the long distance option you are protected from direct attack and may be harder to track. You sort of gain plausible deniability if your drone gets tagged. But you lose a hands on on feel for the situation. Its best for surveillance jobs and the like.
With the on site option (mutual signal range), which can be quite long range in itself, you have a direct connection and don't need to worry about the linking systems dropping off line, can react to things like jamming more immediately and actually see what just dumped you offline (assuming dump shock doesn't disable you). It is best for attack drones and the like.
I'm sure others have their own ideas about how to use these but this is how we generally work it. I can't wait to see how I'm wrong