Are you sure you are selecting the right nodes?
'/html/body//div/ul/li' will select list items, not the list itself.

Given this HTML:

<div>
    <ul>
        <li>one</li>
        <li>two</li>
        <li>three</li>
    </ul>
    <!-- List with 2 empty List Items --> 
    <ul>
        <li></li>
        <li>two</li>
        <li></li>
    </ul>
    <!-- Empty List --> 
    <ul>
    </ul>
</div
[download]

Run on list items, it does delete empty items:

sub delete_empty_list_item {
    my $xhtml = HTML::TreeBuilder->new;
    $xhtml->implicit_tags(1);
    $xhtml->parse_file($file);

    for my $list_item ($xhtml->findnodes('/html/body//div/ul/li')) {
        if ($list_item->is_empty) {
            print qq(DELETE\n);
            $list_item->delete();
        }
    }
    print $xhtml->as_XML_indented;
    $xhtml->eof;
}

OUTPUT:
<div>
    <ul>
        <li>one</li>
        <li>two</li>
        <li>three</li>
    </ul>
    <ul>
        <li>two</li>
    </ul>
    <ul>
    </ul>
</div>
[download]

Run on list elements, it deletes the list itself:

sub delete_empty_list {
    my $xhtml = HTML::TreeBuilder->new;
    $xhtml->implicit_tags(1);
    $xhtml->parse_file($file);

    for my $list ($xhtml->findnodes('/html/body//div/ul')) {
        if ($list->is_empty) {
            print qq(DELETE\n);
            $list->delete();
        }
    }
    print $xhtml->as_XML_indented;
    $xhtml->eof;
}

OUTPUT:
<div>
    <ul>
        <li>one</li>
        <li>two</li>
        <li>three</li>
    </ul>
    <ul>
        <li></li>
        <li>two</li>
        <li></li>
    </ul>
</div>
[download]

You could combine the two if you need to delete both empty items and empty lists.