I say Aye. BUT - if we put a lot of tools in same folder, we will have a total mess with hundreds of files in the same place. We cannot make subfolders due to the automated scripts, how about instead we'll start a convention of naming folders like "statistics_clustering", "statistics_som", "statistics_misc", etc. This is instead of having subfolders "statistics/clustering" "statistics/som", so the automated script would work as is. It would also improve build times due to smaller dependencies constraints.
Just to add a caveat: having more modules can (if the module dependencies are sparse) decrease incremental build times however it does increase the amount of time it takes scons to startup each time you run it (since it has to scan all the files) and increases the amount of time a clean build takes since there is significant overhead for each swig wrapper. Just something to be aware of, I'm not sure where the optimal tradeoff lies (or that there is an optimal value over all the various use cases).
Using scons in interactive mode gets the startup time one of these problems.