I used this a long time ago, and from my observations, the biggest gains occurred in loops. (They are the only time Python is really slow anyway.) However, the last time I checked interfacing with numpy and scipy was not supported.
I would disagree. Cython is less known and has a learning curve. CPython extension interface is well established and more common. That is not an insignificant advantage.
Do you stop for a couple weeks to learn Cython, and do you have complete confidence in its generated code, or do you just start using something you know and is tried and true? It depends. We chose C Python extensions or just writing hotspots in C in a separate process.
The problem of C python extensions is that it is so hard to write correctly because of reference counting.
http://docs.cython.org/src/tutorial/numpy.html
and/or
http://conference.scipy.org/proceedings/SciPy2009/paper_2/fu...
Some types of array addressing will take the slower---but still correct---invocation path through Python, but the common form is compiled to direct (albeit strided) array access.