For now url-encode-url does this:

(url-encode-url "http://www.gnu.org")
   => http://www.gnu.org/

I suggest to not add the trailing slash:

(url-encode-url "http://www.gnu.org")
   => http://www.gnu.org

Adding a trailing slash is only recommended when there is a directory
after the domain name, like in "http://www.gnu.org/software", which
should be written "http://www.gnu.org/software/".

For now url-encode-url is right about *not* adding the trailing slash
in the above case (as this would lead to too many false positives) but
wrong in adding it for http://www.gnu.org, as this disambiguation is
not needed.

Am I missing cases when it is definitely needed?

The following trivial patch changes this.