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ROS packages a custom version of OpenCV3 for Kinetic; it does not use the system version. The opencv3 wiki page describes this and the reasoning behind it in more detail.
I don't think the pre-compiled version of OpenCV3 will have CUDA support, since the pre-built binaries are typically built for the lowest common denominator platform.
Building OpenCV3 from source will probably work, but keep in mind that if you want to avoid ABI breakages and the very strange crashes that they can cause, you'll also need to build everything that depends on OpenCV3 from source, to make sure that it's compatible with your version. At a minimum, this will include the cv_bridge, image_pipeline and image_transport packages.
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