I came across an article on MSDN about location based metadata earlier when I was looking up some info on the scanning problem you raised.
I haven't tested this yet, but it may act the way you want. I'm just firing up a VM to test it now.
Ok, that's spot on what you need to apply metadata quickly! Basically, create your document library and add the columns that you need. (This won't work with lookups though it does appear to work with MMS according to blogs, basically anything with a default value..)
Assign a default value to the columns at the top level, then create the folder structure that you want to use.
Now go into the library settings and click on "Column default value settings". You'll be presented with your folder structure and you can set the default values for individual folders. This metadata will then be applied when you drop files in using explorer view. (I really wish we'd had this in SP2007!)