Searching /r/Latin reveals this thread to hold the answer.

Cunnus, the origin of the English word "cunnilingus," (which was also used in Latin as an insult in its own right in Martial and some graffiti) referred literally to the vulva, but was commonly used for the vagina as a whole. IIRC, there is some instance of the word vagina being used in a Latin text metaphorically, but I can't find any in my current sources, except for its use to refer to husks of wheat.

Interestingly, penis originally meant tail in Latin. cauda, another word for tail, was also used for the penis. penis and cauda both took on more obscene meanings later on, as noted by Cicero. Additionally, mentula was used for a more obscene version, basically equivalent to our "cock" or "dick." Catullus has several poems addressed to someone named "Mentula."