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ROS treats PCL and OpenCV in much the same way; as third-party packages that are built and installed outside of ROS.
I'm not sure what the exact build flags for ROS will be, but if you build and install a version of PCL with CUDA support, you should be able to use that from your ROS packages.
Note that the same caveats apply to using custom versions of both PCL and OpenCV: you will need to rebuild every ROS package you use that depends on OpenCV or PCL. Otherwise, you can end up with different libraries using different versions of PCL or OpenCV, both linked into the same final binary. When that happens, only one version of PCL is used, and any ABI differences will cause hard-to-debug segfaults.
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