Update:
So, ethernet stops working as I described. I remove ethernet from network config in preferences.
After I loaded and unloaded SmallTree kext, ethernet re-appeared.
After restart - ethernet is gone (they are visible, but not working as before).
After manually loading SmallTree kext, ethernet doesn't re-appear.
I delete all FakePCIID and SmallTree kexts and run kext utility.
Restart.
Install FakePCIID and FakePCIID IntelGbx and SmallTree kext using Kext Utility.
Restart.
Ethernet working.
... until it stops working again, as it happened today.
Do it is a problem with kext loading order obviously. I will experiment a bit more, but this seems pretty random. If I rebuilt cache now, I would probably lose ethernet again.
UPDATE:
After CUDA update, Ethernet stops working after restart. I had to remove all 3 kexts, restart, run kext utility an install all 3 again. And after restart it is working again as expected. What could be the problem?