Photon lances collide with everything in their path, right?
I'm not sure if they hit cloaked ships. But yea, that's probably what happened.
Anyway, Don Carsto, it sounds like you're facing a "Spire Hammer" AI, which means it's going to hit you very very hard if you provoke a high-tech wave (Core Raid Engines being one way to do that).
I don't think there's a bug inherent in the cloaked colony being damaged by aoe weapons, though it's possible the colony's max health is some old number that's basically irrelevant in the current balance...
Yep, 400k health, an afterthought. Bumping it up to 5M in the next release
That probably won't save you against a Spire Dreadnought though, those things are incredibly powerful. For those, you need to either not provoke their appearance, or kill them before they get in range of a rebel colony (or anything else you don't want to see very, very dead).
But it should keep a rebel colony from dying "by accident".