I take a look at that and the difference is that when Advanced Tags & Prefixes is enabled the <span> of prefix contains the template Core > Global > Prefix
{{if $text}}
<a href="{url="app=core&module=search&controller=search&tags={$encoded}" seoTemplate="tags"}" title="{lang="find_tagged_content" sprintf="$text"}" class='ipsTag_prefix'><span>{$text}</span></a>
{{endif}}
This template was update in .17, to add the condition {{if $text}}
And when I disable the app, the span doesn't contains this link.
This template is called in Forums > Topics > Topic at line 70
{{if $topic->prefix() OR ( $topic->canEdit() AND $topic::canTag( NULL, $topic->container() ) AND $topic::canPrefix( NULL, $topic->container() ) )}}
<span {{if !$topic->prefix()}}class='ipsHide'{{endif}} {{if ( $topic->canEdit() AND $topic::canTag( NULL, $topic->container() ) AND $topic::canPrefix( NULL, $topic->container() ) )}}data-editablePrefix{{endif}}>
{template="prefix" group="global" app="core" params="$topic->prefix( TRUE ), $topic->prefix()"}
</span>
{{endif}}
In the prefix template, $text is the second parameter
Hope this will help you!