There is only one Droid Control Ship for them to destroy. After the invasion was complete, the majority of the Trade Federation ships left orbit. They no longer had to be there as the invasion was declared legal/ignored, and all of Naboos military might was removed.
The sole DCS left controlled all of the droids. Later attacks avoided this amazingly stupid critical failure point by making the droids independently smarr. At the cost of them being individually dumber. (These are the same people who came up with and implemented the technology of the Death Star. War strategy and foresight seems to be very low on the list of important things for them). OOM battle droids replaced by B1 Battle droids, Roger roger.
The reason the droids didn't attack a second time is because the Trade Federation had already invested a lot of capital in this attack and could not or did not want to spend more on another illegal and likely to fail attack. They lost the element of surprise and were losing favor with the senatorial government afterwards. More importantly, they were just pawns of Palpatine/Darth Sidious, and the whole invasion was just a part of his plan. Once he got what he wanted, there was no reason to continue supporting the attack. He had the Trade Federation move on to other targets in his long plan to gain control of the republic. Naboo was now an insignificant stepping stone of little strategic value.