ATLAS/BLAS/LAPACK is mostly useless for basic sparse operations, at least in scipy. It becomes useful for more advanced operations like SVD, etc... Unless you can use dot (scalar product), which is very fast in numpy if you use atlas (e.g. time the difference between np.sum(x * x) vs np.dot(x, x) - sum does not use atlas, dot does).

For sparse SVD as I implemented in scipy, even fast dot does not seem to make that much of a difference (would be interesting to do real benchmarks, though).