After Effects uses the GPU for almost nothing.
The only feature that depends on CUDA on Nvidia cards is one that you very likely don't care about: GPU acceleration of the ray-traced 3D renderer.
Details are here:
Read the note labeled IMPORTANT there.
This is correct but the GPU is only used for Ray-traced rendering, which was a nobel experiment but is no longer being developed. C4D, included with AE in a lite version does the 3D thing much better than the Ray-traced rendering option. If you are using CS6 or CC and you want to do some of the Ray-traced rendering tricks try the AtomKraft rendering engine.