>Probably the name stuck thanks to this amazing satire of a js library. http://vanilla-js.com/

Using "vanilla" to describe a standard, unmodified and un-customized version of something is a very common idiom. This satirical website followed the convention, it didn't coin the expression. I don't think it's even jargon, it's just based on the meaning of the adjective "vanilla":

Lacking adornments or special features; basic or ordinary: "a delicious twist to a vanilla plot" (Ian O'Connor).