If the user checked the "Create a start link on desktop" option during install, when LO is uninstalled, if it is the only item in the Desktop folder (either All Users or under his profile) the Desktop folder itself is deleted.
Deleting the containing folder when the folder is empty is ok for the Start Menu group, but not for the Desktop folder.
Thanks for bugreport
Please, verify if in last version of LibreOffice still reproducible
Andras Timar committed a patch related to this issue.
It has been pushed to "master":
fdo#44565 do not delete empty Desktop folder on uninstall
The patch should be included in the daily builds available at
http://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More
information about daily builds can be found at:
Affected users are encouraged to test the fix and report feedback.