Annotations were also used to correct errors in educational videos after the videos were published. The errors are still there, but the corrections are gone. They replaced annotations with "cards" which are 100% spam.
E-mail is also often misused for spamming purposes, and Gmail -- which is easy to sign up for and trusted by mail servers worldwide -- is often used for scams. Should we expect it to be terminated as well?
Any solution that allows you to write stuff on the Interwebs can be misused for spam. The solution that every company is expected to come up with, of course, is a good anti-spam mechanism.
Youtube annotations were a solution offered for free. It probably didn't make any sense for Google to implement a good (and expensive) anti-spam mechanism for it. But let's call it for what it is -- a cost-cutting measure made at the expense of users, most of whom are non-paying. There's no point in bringing up technical matters, there aren't any.
If you found them annoying you could always disable them, I was rather fond of them, people did lots of cool stuff with them. Like choose you're own adventure videos, and 3kliksphilips CSGO skin showcase videos. I think they should have kept them. They kept bitching about them not working on mobile but that's only because they chose not to support mobile