For command line scripts there most likely will not be much difference unless each invocation invokes all files in the module, in which case there will be a slight performance cost as n files need to be opened vs one.
For mod_python there most likely will be no difference as byte-compiled modules stay alive for the duration of the apache process.
For google app engine though there will be a performance hit unless the service is constantly used and is "hot" as each cold start would require opening all files.
