I'd take that with a grain of salt. Apple likes to threaten removal of technologies they have deprecated as a way to increase adoption of their replacements but rarely if ever go from deprecation to removal so aggressively, at least on the Mac.
They might exclude deprecated APIs from the pre-announced iOS-MacOS portable platform (Marzipan). That is the move that makes them unsuitable for future use.
This also includes UIWebView and other quite popular pieces of the SDK.
A clean cut - good opportunity to shed some weight, actually.
Note that Apple is still committed to supporting WebGL in Safari, so OpenGL ES will at least be supported that way going forward.
So it's arguably not so much "OpenGL is going away" as it is "OpenGL is going to be maintained by the Safari team, and JS will be the only interface to it" :)
WebGL does not require OpenGL implementation.
Most browsers on Windows use DirectX instead and the games consoles also only have their own 3D APIs.
WebGL is an OpenGL implementation. On Windows, it's often implemented with ANGLE, also an OpenGL implementation.
The GL spec doesn't require that the hardware or OS manufacturers are the ones to implement it. :)
Regardless, “deprecated” means “no longer maintained”, meaning that if any regressions will appear in the near future, it’s possible no one will fix them, as these issues will not be prioritized.