I genuinely don’t believe it. They’re not using the native video player in their apps. If they can overlay controls they can overlay annotations.
What about the mobile site?
There's no NPAPI plugin required for desktop users to view annotations. All of YouTube works using standardized web tech, and mobile browsers and desktop browsers are the same underlying engines with different chrome. There's no technical reason why annotations couldn't work on the mobile site, though from a UI perspective you'd need to size them appropriately for fingers to interact with. It's not that Google can't, it's that they simply don't want to.
That's not quite true. If you want to view the video in fullscreen on iOS it'll just show the content of the video tag and nothing else. They're working on Fullscreen API support, though.