Amusingly enough, Fabien Nicieza; the writer who co-created Deadpool (alongside much-loathed artist Rob Liefeld) has admitted that the character's secret identity is something of an in-joke.
When Liefeld presented the character design to Nicieza as a character to intoduce in the now-defunct series The New Mutants, Nicieza accused Liefeld of simply wanting to make use of his own version of DC Comics character Deathstroke the Terminator. Liefeld admitted it, and so Nicieza decided to name Deadpool "Wade Wilson", in homage to Deathstroke's real name: "Slade Wilson".