I’ve heard it called a hoo ha, but not a hoo hoo, and I have certainly never heard a penis referred to as a hoo ha. Willie or wee wee or a winkie or any number of other things, but I’ve only heard a vagina referred to as a hooha. The Urban Dictionary says it is East Coast slang, but doesn’t really offer much in the way of origins. They also mention hoo-hoo as slang for vagina.
With slang, it’s hard to get origins, I think. Plus it’s hard to nail down the meaning, since the usage is so varied. Maybe over time, things will harden a bit, and usage will be more specific and stable.
Perhaps the word comes from the sounds some women make when their hoo-has are being pounded in a delightful way?