The SMBC comic from a few days ago goes like this:

Something didn’t seem right about the whole thing but SMBC is usually grounded on at least some fact, so I decided to explore, and it turned out to be more interesting than I had earlier thought.

It turns out that the term vanilla (used to describe the beans) does come from the Latin root vagina, but it’s not as simple as that.

In Latin, the word vagina meant just a sheath or a scabbard (kinda makes all those dick jokes funnier, eh). The Latin word wasn’t used in an anatomical sense in classical times. As usual, we turn to our friend EtymOnline

[vagina (n.)][1] 1680s, from L. vagina ”sheath, scabbard” (pl. vaginae), from PIE *wag-ina- (cf. Lith. voziu ”ro cover with a hollow thing”), from root *wag- ”to break, split, bite.” Probably the ancient notion is of a sheath made from a split piece of wood (see [sheath][2]). A modern medical word; the Latin word was not used in an anatomical sense in classical times. Anthropological vagina dentata is attested from 1908.

In Spanish, we get vaina which comes from the Latin vagina, and means more or less the same thing—sheath/pod. The diminutive form of _vaina_ in Spanish is vainilla. The diminutive form of a word is usually a form that expresses a smaller version of the same object. Many languages use diminutive forms as terms of endearment. In Hindi, for instance, you add -u to names to make ‘cuter’ versions of those names. E.g. Rajiv —> Raju, Nishant —> Nishu, and so on.

Vainilla then means small pod, and this was the word the Spanish and Portuguese explorers chose for the Vanilla bean. This was also used for its scientific name Vanilla planifolia. That’s how Vanilla came to English. And EtymOnline agrees—

[vanilla (n.)][3] 1660s, from Sp. vainilla ”vanilla plant,” lit. “little pod,” dim. of vaina ”sheath,” from L. vagina ”sheath” (see [vagina][1]). So called from the shape of the pods. European discovery 1521 by Hernando Cortes’ soldiers on reconnaissance in southeastern Mexico.

It is interesting to note that, although vanilla does indeed derive from the Latin vagina, it has nothing to do with the female reproductive organ of the same name, because it evolved with the sheath/pod meaning all through. In the meanwhile, the same Latin term got co-opted into English for referring to the sexual organ, this time having nothing to do with fragrant beans. Putting it all together—

There’s another interesting thing here: how the SMBC comic changes the head of the modifier little. Even if we take vanilla to refer to the sexual organ, the diminutive form would imply that it means little vagina. However, when the character in the comic summarizes Vanilla Sex as a little vaginal sex, it makes little modify _sex_ instead of vagina, giving it the sense a bit of vaginal sex, instead of sex with a small vagina, which is what vanilla sex would technically mean if it were indeed derived the way SMBC claimed.

Which brings us to the main premise—the term vanilla sex. It is clear that vanilla here refers to the ice-cream flavor, and again, EtymOnline confirms—

Meaning “conventional, of ordinary sexual preferences” is 1970s, from notion of whiteness and the common choice of vanilla ice cream.

The use of the word vanilla as an attributive modifier meaning plain / commonplace / whatever you would typically expect / without any additions / bare minimum is fairly common, and refers to the ubiquitous vanilla flavor of the ice-cream that is often used as a base flavor. I did a quick search for vanilla [n*] (which would search for the word vanilla followed by a noun) on the Corpus of Contemporary American English (referred to affectionately as COCA) and I am listing a few varied examples of vanilla used in the sense I discussed—

A sense that you had a feeling that somebody thought you were this sort of middle class vanilla girl, and you needed to break free of that image (1998)

Good, high cheekbones, a kitteny little nose, playful blue eyes — a vanilla princess through and through. (2011)

I have what I consider a very vanilla personality. I just show up and do my thing. (2007)

But they supply the only red glare in a show that otherwise reduces a war to a vanilla pageant. (2009)

The reel looks nice but delivers a vanilla performance. (2010)

“With a plain vanilla name like Jones, you got ta have a first name that’s special,” she’d said (2007)

“It’s an NGO,” Mr. Murphy said. “Just your plain vanilla NGO that does aid work.” (2005)

And finally, IIT Bombay calls its basic BTech curriculum (without Minors, Honors or any other courses above what is mandatory) a vanilla curriculum. As any IITian would attest, it rarely involves vaginas, small or otherwise.

(Hat tip to Raja Vinay Chandra for pointing out this comic to me)