Cloaked ships are currently my bane. My problem isn't massive swarms of cloaked ships, it's the 10 or 15 little things that manage to get past the defenses long enough to re-cloak and meander to the relatively defenseless econ planets to blow up the command stations. And then it mocks me. Mean computer.
It's actually not too much more than annoying, or anything the computer hasn't done before. The main problem is the fact you only get four decloakers and that it seems like the computer guns for them first now. Ultimately, that that whatever gets past the tachyon turrets long enough to re-stealth becomes unfindable unless you use drastic measures like warheads (progress=bad) or using a ton of knowledge for a Mark III military station.
On the flip side, I don't currently find cloaked ships to be very useful, although I'm remaining stubbornly loyal to my precious autocannon minipods. The computer always seems to instantly find my cloaked stuff, so springing their own tactics on them isn't all that effective. You can take out the tachyon guardians with raid starships or a force of ships, but if you've got enough stuff to do that, you might as well just use the normal force to blow up whatever you were going to send your cloaked ships at.
Also, in the last game we were playing, I was running around with the Mark IV scout and found an ENTIRE PLANET that was cloaked. Including the PLANET ITSELF. Seriously, the planet was a big cloaked circle that you could see stars through. That made my day. Hee.