Apple also, I think, offers trade-in for the devices, recycling the components and preventing them from becoming e-waste if the device is a total loss.
They're under no obligation to replace your motherboard with a "new" one, so it's possible that it goes back to the repair depot for actual diagnostics and repair by better trained and equipped technicians.
I have no idea, maybe they do just shred it and melt it down, but it sure doesn't seem efficient for Apple to simply toss the motherboard rather than try to repair it themselves, otherwise the repair would be vastly more expensive -- AppleCare or not.
If they didn't, their own warranty and repair program would be a money black hole.
It's definitely a frustration for upgrades - but not really reliability anymore. When's the last time someone complained their phone's SSD died?