Humor has it's place in Zelda, but there are plenty of better ways to make the games funny than raunchy adult humor.
Toon Link in Wind Waker, for example, had a number of funny moments that serve as a good example of how humor should be used in Zelda. I particularity like the scene where he freaks out at Tetra's plan to launch him into the Forsaken Fortress with a catapult. His shocked expression, the way he squirms in the barrel as Tetra look's on and his final scream as he's launched through the air only to land splat against a stone wall, all mixed together to create a charming comedic scene.
Zelda in general has no shortage of humorous characters and clever dialogue. I personalty thought Groose's portrayal as a pompous lovesick goof in Skyward Sword was a riot. I think this kind of humor, based off outlandish personalities and situation comedy, is a far more effective way to integrate humor into the series than jokes.
Also, somehow I don't think Ghirahim's appearance and behavior in Skyward Sword was meant to be humorous. If anything, he was meant to freak people out who couldn't handle how fabulous he was.