According to the novels (Not sure if they are classified as canon so don't kill me) the Other is known by her adviser (Lord Falak, I think?) and a few of her high up staff and generals, and nobody knows how powerful the Jove Observatories are right? Who says they can't detect a sig spike in New Eden when something that psychically powerful hits? Or can't register stuff like that? Who says they dont monitor the people of New Eden? Or have a back door into the CONCORD/CAPSULEER network? If they did they would be able to find a connection somewhere to Jayml being cloned, or a reference somewhere, power spikes that were un registered, who knows?
I mean, think about it, the Jove were the best, smartest, and most advanced people, now, if the Drifters killed them, that means they are better then the Jove, hence more powerful in every way or the Jove would have found a weakness and won, now, using this, is it not plausible that they would have the tech to detect such things? I mean, even in RL we have equipment that can see a heartbeat from 1km away, and that is with a device the size of a iPhone, and we can see someone fart at night from 10-15km away with special THERM vision (I used one once at a Cadet activity with some Armored guys, was awesome!) and we are thousands upon thousands of years behind New Eden if such a thing can even be said.
Also, something people may have missed, there is an Amarrian at the EVE Gate who spoke to and was connected to a Sleeper/Jove Construct/Drone with Jove knowledge, he knew about the Other, who is to say that that information was not saved and sent to the Jove Observatories? I dont know why they would hunt the Other though.. Maybe it is the conscious of someone important or they are afraid it will lead to the people of New Eden finding their weakness, or hell, what if half the Other went into Jayml, and the other half of Jayml went into the Others actual form? Lots of things could be the reason, and as so many say, tin foil hat time.
I can't wait to see, as I loved the books, and got upset once I found out there were no more novels, hopefully if the plot evolves a bit there will be!