Apparently this is handled correctly from the GUI :-) (14.04 LTS)
(Move to Trash, Empty Trash)
But generally: When you have a link to a directory, be VERY sure to delete ONLY the link should/when you come to that point.
From terminal, the correct thing to do is:
rm -r LINK-TO-DIR
... which will first delete the files/dirs that the link MAKES VISIBLE,
and even more so with the "-f" flag.
If you are a "Terminal" user, have a look on the output of
... that ls lover case of LN nothing else ;-)
The syntax for it may seem a tad "backwards" at first as you FIRST specify where it should point, then the name of your LINK.
mkdir -p $HOME/z
ln -s $HOME/z New-Link-To-Home-z
... note that the GUI will not notice the new Desktop content without help; you need to logout+login.
More info on the 'net or slightly terse in either of
... where I personally prefer the first because 'info' has a tendency to 'slip out of context'.