Thanks for this new addition, Rory.
1) I think a new section with tags is nice and tidy, excellent!
2) I think automatic creation of a new subfolder may perhaps create as many problems as it solves (?). As Iain says, some DAWs will then require you to browse to the subfolder before actually opening the plugin. Also, if the user already have the plugin files in a separate folder, we would get yet another subfolder to that structure. With regards to name pollution perhaps it will not be a problem, if the csd code expects to find image.png in the same directory as the csd, then there is probably no other image.png at that location. Then again, it would not be necessary to copy those files (to the same location) on Windows and Linux. Perhaps the copying should be only for OSX?, as that's the platform where the problem with files inside the vst bundle occurs.
Another matter of course would be if we would like to include files from other directories as well. But then it is a bigger project altogether to make that portable and reliable. If the files are moved into the plugin directory, the references to the file would have to be updated in the csd. It would be nice, but only really necessary in the case where one loads a lot of large samples/files and want to be able to not have several copies of those but keep them all in a ../../Cabbage/samples directory or something like that.
.. so in brief, 2) no