i have a "full install" where literally all plug-ins are present, and when i feel i need a clean DAW for a new project, i just make a copy of cubase or nuendo and a small assortment of plugs.
of course this would be a no go with DP and protools.
in my custom max/msp apps i sometimes use auto loading, and mostly use drag and drop. for that purpose my "full install" VST folder is always present as springloaded folder on the OS9 desktop.
also, cubase and nuendo allow to make subfolders, this makes it easy to control a set of 1000 plug-ins if required. but for many years i have not been using subfolders - but renamed all products alphabetically after vendor. it was not slower to find stuff this way, it was often even faster than using subfolders.
about copying, i know no product and no copy protection scheme which wouldnt allow to just make as much copies as you wish?