Currently the only realistic counter to loose stealth of your hidden colonies is to put hidden colonies on all planets of a system.
There are multiple things wrong with it I think:
- it is a build-everywhere building
- it is very powerful for its price (both in RP (150) as in PP), negating one-and-a-half levels of stealth. Plus you get speedup.
- it is too accessible (150RP on top of active radar), by that time the opponent could only have research one level of planetary stealth. And the prerequisite (active radar) also negates one level of stealth. Even great stealth species have trouble with that.
For pacing: make it later accessible, up the research cost a bit
For restricting build-everywhere: make it cost influence upkeep to keep the numbers low. Up the PP cost so that moving the building hurts; or building one lighthouse also costs some influence; or lower influence upkeep the longer the building exists.
And also add a counter: e.g. a targeting computer which makes the ship weapons shoot at marked planets and no other targets. A target is marked if the enemy has lighthouse on it OR if you mark it by building an influence project to expose the defense structure.