Corrected entry: In this episode Dr. Hibbert says the crayon was never spotted because he always covered it with his thumb, but in episode 4-18, "So It's Come to This: A Simpson's Clip Show", when Homer is in the hospital, his head X-ray is placed up on the light box on the wall, and is visible with nothing blocking it, so the crayon should have been spotted then.
Corrected entry: Homer's dumbness is caused by the crayon stuck up his nose, as stated in the episode, but on a previous episode, Homer remembers he once was injected with a new drug which the government was testing, which left him bald, fat and stupid.
Correction: He also hit his head on a coffee table as a child and was brain damaged. There's a lot of reasons.
Correction: The joke in the scene is that there really is no way to explain why or how he would miss a large crayon in Homer's brain after all these years, numerous injuries and many x-rays. Even if he should have seen it, its a character mistake. As you pointed out there was no way he should have missed it but either he really did miss it everytime or is lying to cover up his mistake.
Lummie ★