Do you have cloaked enemy ships in your systems that even tachyon warheads can't find? Take a fleet of ships to an adjacent system and then detonate an EMP warhead in the offending system! Once the nefarious enemy is revealed (the EMP shuts their cloaks off among other things), bring the aforementioned ships back to mop the little gits up. I had Red Cossack laughing in vent the other night when I cleaned out 3 systems of cloaked Raptors this way.
Not that they hurt you or anything, but it's creepy enough just having them sitting around in your system. WATCHING. ALWAYS WATCHING.
Tachyons wouldn't decloak the raptors? Do you have a save of that? Permacloaked things require EMP'ing since they're, well, immune to tachyon. But raptors aren't permacloaked
I made some changes roughly a month ago to cut down on the permanent cloaked residents, like having it auto-detonate stealth tachyon emitters left by the AI when you take the planet. Though I guess those went away with AI turrets.
Anyway, yea, those enemy units permanently stuck on your planets are bad both for OCD players (like myself) and the CPU due to extra processing that your units will frequently be doing ("Enemy! Can I shoot it? Awww" ... "Enemy! Can I shoot it? Awww" ... "Enemy! Can I shoot it? Awww" ...). So I want them gone.
I'm just referring to the truly permanent stuff, as in it's an hour after you capped the planet and the cloaked number is still there.