Interesting.
Could you tell us if you checked Release Notes, did Google mention anything about it?
Or maybe it was one of 'bugfix' patches and now they check if shortcut already exists.
Which browser do you use? If you with a completely new, unused browser, does pop-up appear? I wonder if it is matter of browser or system.
I use Chrome on my smartphone, and I haven't checked what exactly it is because Google very often has updates for its services via Google Play - but that pop-up stopped appearing immediately after updates. I think it's a combination of both, although I didn't make a browser update, there seems to have been a hole in the system through which that pop-up was persistently displayed even though notifications and pop-up ads were blocked.