Well that's embarrassing. I made a change to the pkgsrc check-shlibs scripts last November, and only today realised that the change to the macOS script was incomplete, and has since then been returning success for all checks.
https://github.com/NetBSD/pkgsrc/commit/c42c4487ad4731a83d164a5bc1066759940499e3
A good reminder to thoroughly test changes when writing in non-strict languages!
In related news, the latest mktool implements a check-shlibs replacement and runs up to 30x faster than the awk version.