The only thing AE really uses the GPU for is the obsolete ray-traced renderer. Very few people use the ray-traced renderer. I wouldn't worry about it at all.
Now, some third-party plugins (like Element, 3D Invigorator, ShapeShifter, etc.) DO make use of the GPU, but they'll work with AMD cards and have nothing to do with that CUDA warning you're getting. Check the requirements for any you plan to purchase.
You can confidently tick the option to never show that message again.
Thanks mate thats really helpful.