I'm using GLKit's GLKView in one of my projects. As per Apple's documentation it is deprecated. I can still use it in my app and it is fully functional (for what I want it to do) with latest iOS versions. I'm using it because of an older SDK that I'm using has good functionality for it. What are reasons not to use it anymore?
If something is deprecated, that means they may remove it in future versions. If you continue to use it, your code may break next time you update the library.
They left it in despite being deprecated to give you an opportunity to switch to a new solution.