Shortcodes will always be rendered, even if they’re inside HTML comments. Imagine a shortcode that renders … comments, there’s no way for Hugo to know that this is supposed to be blanked out.
I’m not sure what you mean by “now”, but with this site configuration…
[markup.goldmark.renderer]
unsafe = true
And this Markdown…
<!-- đź’ˇ [More on *my subject*]({{< relref "my-subject" >}}) -->
Hugo has been rendering the shortcode since v0.54.0 (that’s the earliest version I tested). So, with respect to including shortcode calls within HTML comments with the site config above, nothing has changed between then and “now”.