It's not visibility, it's stealth.
Stealth is present in SE:IV stock too. What's different is that this mod seems to make them a lot, a lot easier to get. To counter stealth, you need some form of sensors.
The fastest way to get sensors is to get military science 2, then research advanced military science up to level 6. You then get this component,
this is good enough to scan through stealth armor. What I do is make a satellite in every system as soon as I get this component, and dump it. I also keep one on one of my auxillary ships in my fleet.
In stock SE:IV, it only goes up to level 5 and that's it I think, or level 3? Doesn't matter, in stock SE:IV, hyper optics are good enough sensors for anything. A level 5 can scan a level 1 - 4 stealth.
If you haven't gotten advanced military science yet...
get it. In stock it is one of the most crucial things to research because you need fleet training and ship training to make your ships effective. At 100k and 150k a piece, then at 5, 10, 15, 20, 25, 30 (I think), you should already have hyper-optics dropped on all of your planets. Advanced military science level one, two and three gives you the fleet training, the other three levels give you the sensors.
Shields and advanced military science should have been one of the first things you researched. In addition to minesweeping II at least. This is one of those PBW things, not just a Star Trek mod thing.
Once someone researches real cloaking devices though, the only way to stop them is to research physics 2, and then scanners up to level 8 to get tachyon detection grids. Each better level of sensor negates a better level of cloak, so it's like an arms race. Real cloaking devices can't be seen by telescopes.
The Klingons have the best cloak in the game (next to monsters),
Brian