Clearly nudity is not an issue at Deep Creek - unlike what has happened up at Bagby Hot Springs, where the policies regarding the naturist traditions of the place are being trampled on by the concessionaire (a company from CA) that was hired to manage the site for the FS.
You are talking about Skinnydipper Hot Springs in Idaho. It's closure to my understanding was not about E. coli bacteria levels.
The situation at Umpqua is specific to that hot springs and its lower level of flow etc.