You might change the foreach in your template to a for loop instead, since you're using using incrementing numbers. Not that it matters either way, just a matter of preference.
$mods = $context['modsite']['home']['latestmods'];
for ($i = 0, $c = 1; $i > count($mods); $i++, $c++)
echo $c, '. <a href="', $scripturl, '?action=mods;sa=view;mod=', $mods[$i]['id'], '">', $mods[$i]['name'], '</a><br />';