For the Itemdb.xml, I saw instances of that file in all of my individual pack files, from 164_full, to 166_168; I'm going to go ahead and guess that you extract from the latest pack files? I can't see why there's redundancy there however.
Yes, you do extract from the most recent pack file.
We're on client version 168 at the moment. When we go to what will likely be 169 or 170 pack, we will probably get another itemdb.xml in that pack. That is because the file is updated, so it must be included in the most recent pack with the saved updates for them to work properly in game.
Which also means, the older the itemdb file is, the more likely it will be that the file has less content and will be a small file size. When Nexon gives you a new pack file though, they do not clear out the outdated files in previous packs. So that also means the longer you have mabi installed without getting a new full pack file, the more memory it will require on your pc as, in a sense, all files are archived in previous pack versions.