I am quite stumped what I am supposed to do with outdated machinery. They still take up Karma, so I cannot build new mines and builders, but I found no way to scrap them or rebuild them, or whatever. What am I missing?

Choose the unit on the map. Then click the corresponding icon at the top right hand corner (it says additional functions on mouse-over).
There you can make a snapshot with this unit centered, rename it or dismantle.

Outdated units used to be wiped out automatically and we were receiving a lot of mails like "Where did my wagon go? I don't have any attacks in logs", so we decided to make it the owner's choice whether to leave it as outdated machinery or not.

ahh, thank you

My fireship just vanished. no one attacked it. It was about the time it would be outdated, though. But it's not listed as outdated, just gone.
So here's my inspired guess: Fireships, unlike all other machinery, go up in an annihilating flash of eldrich mandrake fire when they expire.
Am I right?

Cheers

Yes.

You guessed correctly, that outdated freeze only applies to units with an inventory.

So outdated machinery is not functional at all? it just takes up space?

It is fully functional, but you can't move it.

when clickin on additional funcitons mine it says (below rename and snapshot)

You cannot dismantle a loaded transportation vehicle.

but I don't see anything in it and I cannot take anything form it with a unit next to it. It recently outdated

If its a "transport" machinery like HQs, mines, towers, it can't be dismantled until a hero/machinery inside it is loaded out.