Nintendo's president, Katsumi Kimishima about a month ago in an interview with the magazine Game Informer has confirmed that Waluigi is in fact, uncircumcised.
"Waluigi still has his foreskin, you won’t ever see it but it’s there. We do not know why he remains uncircumcised, however. It might be a religious thing, it might not." Said Kimishima. He added: "Also, remember Shy Guys? None of them have any gag reflexes. So you could really go to town if you wanted."