It seems you only want the last time script X accessed your script Y. Not usage statistics like "Y was accessed 2050 times from X".

If that is the case, roboticus solution seems a good fit. On average scripts will use (lets say) 5 modules, so the amount of small files is just 5 times the amount of scripts you have in use.

But if you want usage statistics, the log file seems the better idea. Just accumulate the numbers into a summary file whenever you prune. Another advantage of the log is that you can easily use more than one computer to get statistics from (as it is easy (on linux at least) to send log messages to a central machine)