Installing 11.4-p3 removed files in /etc/ssl/certs. From a zfs diff:
It does not recur if the machine is rebooted, so it was not a rc script that removed it.
You are incorrectly using/abusing this directory. It is solely meant to be used for hashed CA certificate links for be consumed by OpenSSL when verifying a peer. Do not put your certs into it.
*** Bug 250300 has been marked as a duplicate of this bug. ***