The feature which displays the message you saw is behind a site setting (detailed_404). That’s now disabled on Meta, so you will never see it.
I just tried it out locally, and I can no longer reproduce the issue you saw, so I think we’re good. If you try and access a deleted topic with detailed_404 enabled, you will see
I think the original bug you reported was introduced in this commit, but then the feature was overhauled in this commit, which resolved a number of issues.