How much of NumPy and SciPy is in C?

1. I would question any benchmark which doesn't show the source for each implementation (or did I miss something)? It's entirely possible that either or both of those solutions are coded badly which would result in an unfair appraisal of either or both language's performance. [Edit] Oops, now I see the source. As others have pointed out though, it's not using the NumPy/SciPy libraries so those benchmarks are not going to help you make a decision.
2. I believe the vast majority of NumPy and SciPy is written in C and wrapped in Python for ease of use.
3. It probably depends what you're doing in any of those languages as to how much overhead there is for a particular application.

I've used Python for data processing and analysis for a couple of years now so I would say it's certainly fit for purpose.

What are you trying to achieve at the end of the day? If you want a fast way to develop readable code, Python is an excellent option and certainly fast enough for a first stab at whatever it is you're trying to solve.

Why not have a bash at each for a small subset of your problem and benchmark the results in terms of development time and run time? Then you can make an objective decision based on some relevant data ...or at least that's what I'd do :-)

There is a better comparison here (not a benchmark but shows ways of speeding up Python). NumPy is mostly written in C. The main advantage of Python is that there are a number of ways of very easily extending your code with C (ctypes, swig,f2py) / C++ (boost.python, weave.inline, weave.blitz) / Fortran (f2py) - or even just by adding type annotations to Python so it can be processed to C (cython). I don't think there are many things comparably easy for C# or Java - at least that so seemlessly handle passing numerical arrays of different types (although I guess proponents would argue since they don't have the performance penalty of Python there is less need to).

A lot of it is written in C or fortran. You can re-write the hot loops in C (or use one of the gazillion ways to speed python up, boost/weave is my favorite), but does it really matter?

Your scientific app will be run once. The rest is just debugging and development, and those can be much quicker on Python.