The answer would depend on which villain, and which universe you're speaking about.
We are told that Bruce Wayne chose the image of a bat to "strike fear into the heart of his enemies". In fact, everything about his physical appearance is used to create a false image that he is more than just a man. In the movie incarnations, his body armour makes him look more muscular than he actually is, and he uses his gadgets and the fact his armour gives him some bullet-proofing to make people think he can fly and is immortal. None of this would "strike fear" into anyone if they all knew he was just a guy in a suit, so all of this suggests that most of his "enemies" are supposed to believe that he has supernatural powers.
That said, Batman's primary purpose was to fight crime on the streets of Gotham. The image he created is primarily aimed at the "street" criminals - thieves, murderers, muggers etc. Super-villains are a different case, and many of these have (in various universes) discovered his identity, including Bane, Deathstroke, Despero, the Riddler, Hush, Man-Bat, Max Lord, Ra's Al Ghul, Owlman, Killer Moth, Lex Luthor, and Joe Chill.
A good example of this contrast between how "regular" and "super" criminals view Batman is found in the 1989 movie, in which the regular criminal 'Eddie' talks about "the Bat" killing his friend 'Johnny Gobs' and sucking all the blood out of his body, showing that he believes the supernatural stories; whereas The Joker describes Batman as "a man dressed as a bat" with a collection of "wonderful toys".
Of course, knowing his identity isn't necessarily the same as knowing he doesn't have any powers; but some of these stories have involved villains knowing his identity due to telepathy (Despero, for one), so arguably they would know both.