Thank you for your bug report, it works correctly on the current Ubuntu
serie. nautilus uses libarchive but that package didn't change in focal,
unsure why it was working and isn't anymore for you...

** Changed in: nautilus (Ubuntu)
   Importance: Undecided => Low

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https://bugs.launchpad.net/bugs/1917812

Title:
  extracting archives from within nautilus omits subfolders

Status in nautilus package in Ubuntu:
  New

Bug description:
  When extracting ZIP archives from within nautilus (e.g. right-click ->
  "Extract Here") the extracted file structure is missing subfolders.

  Reproduce:
  1. download a ZIP archive that includes files and folders in the root (e.g. 
https://github.com/electron/electron/releases/download/v12.0.0/electron-v12.0.0-linux-x64.zip)
  2. within nautilus right-click on the archive and select "Extract Here"
  3. check the extracted folder, you will see that only the files have been 
extracted, the folders are missing

  This is an issue that was recently introduced, as this used to work a
  while ago on Ubuntu 20.04.

  ProblemType: Bug
  DistroRelease: Ubuntu 20.04
  Package: nautilus 1:3.36.3-0ubuntu1
  ProcVersionSignature: Ubuntu 5.8.0-44.50~20.04.1-generic 5.8.18
  Uname: Linux 5.8.0-44-generic x86_64
  ApportVersion: 2.20.11-0ubuntu27.16
  Architecture: amd64
  CasperMD5CheckResult: skip
  CurrentDesktop: ubuntu:GNOME
  Date: Thu Mar  4 22:09:52 2021
  SourcePackage: nautilus
  UpgradeStatus: No upgrade log present (probably fresh install)
  usr_lib_nautilus:

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