PyInstaller maintainer here.

PyInstaller includes a "hook" for adapting it to the special needs and methods of numpy. This works quite well, anyway if numpy changes, it might take some time until PyInstaller catches up.

PyInstaller 4.0 (released a few weeks ago) added support for package developers to provide hooks with their packages. Thus numpy could deliver hooks including or excluding modules and files as needed. If you are interested in providing PyInstaller hooks with numpy, please have a look at package developers to provide hooks with their packages.