That’s quite an adventure. 
As to why it happened, I’m not sure. Recently the archlinux-keyring and manjaro-keyring packages was updated. But so far only in Unstable branch.
The tip about pacman-init.service is a good one. It was used by manjaro-system package to regenerate the keys on a previous update. But I fear that the standard keyserver used in gnupg is having issues these days, which results in lots of errors when populating keys.