I am using xfce gtk3. The xfce applications menu does not display any of the category icons and whiskers menu does not show the categories at all . I believe that there are permission issues due to the fact that when I run Xsession as a root user (I know it is not recommended) the icons appear . I don't have any files under '~/.local/share/desktop-directories' that may override default files. Permissions of '/usr/share/desktop-directories' are 'drwxr-xr-x 2 root root' . Permissions of files in the directory are '-rw-r--r-- 1 root root '.
It appears that the problem was that permissions of '/var/lib/flatpak' was messed up and desktop directories didn't pass corectly . Changing permissions to 755 fixed the problem.