In #34918, a exact duplicate, there was discussion that followed a different approach than the one on this ticket. Therefore, while closing #34918 as duplicate of this ticket, I've updated this ticket's description with some information the other had, and will quickly summarize the patches + discussions of the other ticket, as it took a different approach to solving the issue.
It was pointed out that hiding the comments of post types that don't exist/inactive would make them inpossible to edit or remove. It was then noted that while this was likely by design, WordPress does not show posts from unregistered post types, and thus this served as an argument to hide comments that are orphaned.
The ticket consensus then agreed that it made sense to hide posts if the post type they are connected to is "gone", particularly from a consistency standpoint.
Component maintainer, @boonebgorges agreed to this approach (https://core.trac.wordpress.org/ticket/34918#comment:10), and then a patch was produced (attaching it below) that hides the errors in the comments list table by checking to see if the post type object exists. This patch however, did not address the implications of a plugin using a wp comment query or the dashboard widget.
Notifications from old ticket: @Funkatronic, @jdgrimes, @lukecavanagh, @nekojira, @obrienlabs, @wesm87