Billy Blaze has an I.Q. of 314. How can he not figure out a simple substitution cypher?
At the start of Keen 4 (the beginning of "Goodbye Galaxy"), he has to stun his mom to keep her from seeing his spaceship and then his dad to keep him from finding mom! So by the time he finds the letter, Billy is perfectly able to crack the cypher, but is in a SERIOUS hurry to get home. Per the ending text: "Keen takes the note with him to decipher on the long space voyage home, not seeing anything else of interest"...including his rival's helmet on the floor. And as he's a young child worried sick about the parents he zapped with his stun-gun, he promptly forgets all about the note on the way home.