If you didn't know already there are Python bindings for Godot. It is possible to access external libraries, but they must be included with the Python libraries in the Godot game project directory. For example, the Godot project with the Python bindings would have the
pythonscript directory, as well as the necessary *.py files. The external library is placed with the libraries the Python add-on uses. What external libraries you can use, though, seems to be limited. For example, NumPy would have to be placed with your Godot project's Python libraries. When exporting, the C language parts of NumPy would have to be built and distributed with the project for the target platform. PyQt, though, is a bit more tricky, as this depends on the Qt bindings for Python, and will require either distribution of the Qt bindings, or detection of said bindings for the target platform. That process in itself could require platform-dependant code (e.g. a Bash shell script to detect the Qt bindings), or could even require GDnative code.
I hope that this answers your question.