One possibility is that the old simile describes the whistling sound of a sword as it swishes through the air to decapitate someone, and an early 19th century quotation does suggest this connection: 'A first rate shot.(his) head taken off as clean as a whistle.' The expression is proverbial, at least since the 18th century, when Robert Burns used a variation on it. More likely the basic idea suggests the clear, pure sound a whistle makes, or the slippery smooth surface of a willow stick debarked to make a whistle. But there is also a chance that the phrase may have originally been 'as clean as a whittle,' referring to a piece of smooth wood after it is whittled.