Surely licensing can't be the reason. Firstly, there is no distribution happening here - a plugin written against the Blender API and shipped separately is no different from NVIDIA's proprietary driver for Linux.

The usual GPL issue around plugins is whether program+plugin are a "mere aggregate" or a "derivative work". This doesn't really matter if they aren't distributed together, but even if it did, the question is no easier to answer in the case of interpreted vs compiled code. They are still running in the same process, exchanging internal data structures through direct procedure calls. It just so happens that one is running through a translation layer.

If that translation layer protects you, then you could just as easily enjoy that protection by running binary plugins through a no-op emulator.

And regardless of all of this, there's no reason Blender Python plugins can't use Python native extensions for performance. FLIP Fluids, for example, has a C++ fluid sim engine and uses Python just for the interface to Blender.