Duplicating the data/info is generally not a good thing to do, though sometimes it is convenient.
You have configuration and log files. You have no choice about how these are organized - they are as the respective software requires or produces them.
You are trying to produce some results, which you haven't described but which are likely to be very relevant to answering your questions about how best to organize your data.
Are you storing the data somewhere (i.e. after analyzing the configuration and log files and producing summaries, stats and graphs, are these stored in a database of some sort? Or are you producing them "on-the-fly" each time you want them?
Once you have your data structures, how are you using them?
How is having the nested structure a benefit to what you are doing?