From my experience, i have yet to hit the API ban using Google Drive and Stablebit, i have a very large library. My Movies library is setup into sub folders as you suggested. I have done full library scans to test this specifically for a API ban.
As to answer your cache question, Plex of course would have to rescan your library of your files again due to path location being changed. So yes i would guess that it would update the cache to reflect that.
As i said above, i have yet to hit any kind of ban with Google and Stablebit, if you do some how achieve hitting a ban, please post and let us know so we can keep track =).