Literally in hebrew the word meaning cunning and the word meaning naked are interchangeable.
According to the Tikkunei Zohar, (Tikkunim #57-63 approx.) when HaShem created the forces of darkness, He didn't leave time to create clothing for them, so hence the Snake was naked.
It was the Snake's nakedness that made him jealous of Man, because, as the Zohar explains, at the time when HaShem would have been creating the clothes for the forces of darkness, He was instead creating Adam.
Adam was originally clothed in clothing of light. The Snake was jealous of these beautiful vestments. The result was that he tricked Hava and Adam into losing their clothes of light.
The irony that I noticed this time around is that HaShem then clothes Adam and Hava in clothes of leather. (or literally 'skin') The Zohar explains that these physical bodies we inhabit now are called "The Skin of the Snake."
The Snake's treachery leads HaShem to create the Snake's Garments which He hadn't made previously, but instead of the Snake getting to wear them, Man got them instead. Either way the Snake is still naked.