Hmm.. I think if you use the term naked, in not a sense, I sit naked while posting on Sherdog & see naked more ass bare & not nude it makes more sense. The rear choke, is naked from using a gi, a piece of equipment or any other object you could utilize to choke.
Other chokes that come to mind such as the triangle, side choke or gi chokes need to use the gi or pressure with a trapped arm.
Think of the saying, to the 'naked' eye. E.g. To the naked eye, this person did not see the scam. That gives me connotations of the person with the naked eye, being unassisted, unknowledgeable & deceived. How this works into a choke? Well, a naked choke. you are not assisted & this type of choke is know by anyone, a caveman, a white belt or your girlfriend, so I suppose there isn't much knowledge into the technique.
That or maybe it originated by someone being choked to death at a nudist beach.