The adverb so has as its general meaning “in this manner.” The intensification sense is just one use of the adverb. My guess would be that the form is a combination of so [intensifier] + so [in this manner]
The English so-so is cognate with the German so so, the Dutch zoo zoo, and the West Frisian za za. So borrowing from these languages is certainly possible. I don’t know the history of the term in these other languages.
Also, the Old English swa swa is an extremely common construction, although it doesn’t carry the same meaning as the modern so-so. Instead it means, “where, when, so soon, as soon, unless, although, yet, if, as if.” So the reduplicated form has been around for a very, very long time.