Reader George B. had written in with the following meme, which is popular, and wanted to know what the answer to the meme was.
Comic book companies did not like to acknowledge the male comic book characters had nipples until the 1970s. So belly buttons was a whole other deal.
Phil Jimenez is detailed in his drawings of shirtless Wolverine in New X-Men #148, but, the belly button is more suggested than drawn.
So, why does Wolverine have a belly button?
The biggest answer is that Wolverine, like all other mutants, did not get his powers until he reached the age of puberty. It is puberty but it can also be triggered before based on stress as shown in Wolverine:
The Origin #2…
Wolverine’s body was seared to the skeleton in Wolverine #43 during Civil War and bounced back to normal.
So, it works like this: he is born, the belly button scar is there, he grows up, and his powers kick in, and that is what he heals back to. So, had Wolverine lost an arm when he was five, he would be the default state that he may just return to when he healed.