This is just a total guess, so sue me if I'm wrong.

A planet's loyalty or whatever seems to determine the resource output effeciency, which makes sense. I believe it not only affects the taxes, but also the crystal and metal, i.e. 50% loyalty would only net you 50% of the taxes you would normally collect, as well as 50% metal/crystal.

Anyway, when you lose the planet, I'm guessing that the metal and crystal production has to be slaved to another planet. So either the AI picks another one of your worlds to attach that production to (which may have a higher loyalty, thus netting you higher resources), or more than likely it simply defaults the loyalty on those resources to 100%, since they lost their planet.

Can a dev confirm this?

I'm going with Durikkan on this. An interesting catch, still

The gas giants thing is a little weird too, I've had a gas giant extractor in the heart of the enemy empire, and yet, I still get 100% of its income.

Interesting observation. It seems to that if culture is the only alternative to bombardment for acquiring planets, you should loose all of the orbital structures on a planet when it defects from your empire.

Would such a result be unbalancing?

I agree with Kade, but what if the orbiting structures just became neutral, ceased supplying resources, and became the property of the next colonizing empire? That could still be problematic I suppose, since you would lose planetary resource income after a successful siege frigate attack, and you might need those resources to retake the planet and recover within a reasonable amount of time.

I guess the problem still boils down to the much-reviled siege frigate spam strategy, which makes glassing a planet too easy. I don't feel like it's a bug, just an unfortunate consequence.

-HD