MATLAB has a TON of things that you don't get with Python + Numpy + Scipy. Complicated plots/graphics with interactivity are a pain point in Python compared to MATLAB. Similarly, the debugging capabilities in MATLAB are truly magical compared to a pretty terrible experience on the Python side of things. Even though we deploy software in Python, we are much faster prototyping in MATLAB and deploying finalized algorithms/software to Python than trying to do everything in Python from the get go. MATLAB's JIT is also pretty great and while Numba is pretty great, it still requires more work and can be brittle at times.
And then there's LabView, used widely for lab and process automation, which really has no open-source or free alternative.