They can build jumpgates? Now that is disconcerting...
Can they probe them down or do they only see them if you lead them there?
Invaders can. One of their smaller (heh) classes of ship is nothing but a grav scout. if you don't chase them down and spot them, they will find all the jumppoints in any system they get into, and their heavier ships will make their way right onto your doorstep. This is what makes an
invader wormhole such a serious problem no matter where it opens on your map. The ships they spawn in that system don't stay in one place once they've scouted their way to your property. One thing I have found, however, is that they're really bad about moving around if you're on top of killing their constructor ships. I had one game that had three (!) wormholes open within the span of a year or two in one system just off sol's doorstep, and by the time I finally cleared out the system I had something on the order of half to three quarters of a million tons of dead enemy military shipping lying around the system. But they never tried to put one warship into sol, despite me blowing up half a dozen gate construction ships that came through the jump point. I was throwing spoiling attacks into the system regularly trying to thin down their numbers , but they clearly knew the jump point was there and my attempts to thin them out never really met with great success until the very end. I shouldn't have been able to doorstop a major offensive just with a couple obselete laser corvettes picketing the JP.
I've never seen swarm scan down and transit JPs, though I've heard stories of how bad it can get when they do decide to do so on their own.