When I played vanilla, I would see domain probes very commonly, especially if I took exploration missions as the majority of them wanted you to go to some.
However, in my current game after installing multiple mods, including Tyrador, DME, Unknown Skies, and Nexerelin which might affect the fringe the most, I have yet to see a single domain probe/ship/mothership even after exploring half the sector. Of course it might also just be bad luck, but I think one of these mods, or any others that affect fringe generation, might have something to do with it.