In ART, the Zunker Terminus was discovered '17 T-years earlier', from the Idaho end, despite being in a previously-inhabited system.
But since the resonance zone of a terminus is fairly large and very lethal, how could the mysterious ka-splatting of any ship trying to leave on a certain bearing not be noticed? Even very poor systems tend to get quite a few ships a year.
[pre-posting edit thing]: I just realised that if termini aren't usually on the system ecliptic, there's very little chance of people running into them and the area to look in is much bigger. That said, the Manticoran one seems to be and I can't remember any that explicitly weren't.
In fact, given the ridiculous value of a hyper bridge - let alone a junction - and the relatively trivial cost of hyper travel (shipping vast quantities of basic foodstuffs is economically viable), why aren't there companies on the Axelrod line that go out looking for the things? Just have your dispatch boat make a few jumps around the hyper limit, and see if it explodes.

Even smaller systems could pay to hunt down termini - hyper travel is cheap, so the added cost for leaving on a non-least-time bearing can't be very great. So you can pay merchants who were coming anyway to go a few degrees off their normal path, and have the entire circumference* covered fairly quickly.
*See italicised bit, this is where I realised I was assuming they were typically on the ecliptic.