I finally found out the issue! It turns out it has something to do with
xdg-user-dirs.

When Ubuntu was first installed, it created the usual xdg-user-dirs such
as Desktop, Documents, Downloads, etc. etc. It also creates a Templates
folder, for which I have no use. However, I like the little icon it
shows, so I change its name to Temp and use it as a temporary folder
(stores anything I'm working with temporarily).

Once I restored my backup and moved the old contents of Temp to the XDG
Templates folder (which now was also called Temp), nautilus spiked 100%
CPU usage and became unusable! My old Temp folder has 26,732 items,
totaling 334.6 MB. I don't know if it is the number of items or the
overall size that triggers the behavior.

Can any developer try this and see if they can reproduce the issue? For
now I'll just delete de Templates folder, move my old Temp back to ~/
and assign it an emblem, which will end up being the same for me, just
without the 100% CPU issue :)

Thanks again!
Vítor

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https://bugs.launchpad.net/bugs/758522

Title:
  Nautilus unusable: every action takes CPU usage to 100% and freezes
  the UI for 10 seconds

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