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Hi there!
I would recommend to create a ROS package for both libnabo and libpointmatcher until they become "first class" dependencies packaged on most of the major Linux distributions.
I recognize that it is preferable to have system dependencies over ROS dependencies, but do not forget that there is other Linux distributions that Ubuntu. What about the Fedora users for instance? They would still have to build and install your dependencies by hand.
The only other solution would be to use the ability in rosdep.yaml to put arbitraty shell code to download and build the package on non Ubuntu platforms. This is wrong for many reasons :)
Therefore, the only other solution is to package the dependencies as ROS packages. It is easy to do (look at this for instance) and it will ensure that all ROS users will be able to use your package.
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