The seowon in Civ IV was a university replacement that gave an additional 10% science so that's not quite right. And they were basically preparatory schools first, even if steeped in Confucian ideals (which is true of modern Korean education anyway, not that it lessens the scientific or educational impact).
As far as literacy goes, again, that was true of ancient China and Babylon and Egypt as well. Education was generally for the scions of the wealthy and powerful. If we look to access to education among most advanced ancient societies you won't find pretty results. To me this whole access to education point is neither here nor there. A nation's scientific output isn't measured purely by literacy rates or access by commoners to education, if admiration for Babylonian mathematics (and the portrayal of them with science bonuses in Civ) is any indication.
"Modest scientific contributions to the world"? I'm skeptical that if we restrict science-based civs to those that made massive contributions we would get anything other than China, Arabia and the US, among a few others. And I've already pointed out the huge Korean technological influence on Japan, particularly in the wake of the Imjin Wars. I would hardly call their contribution to Japanese printing popularity "modest". I also don't think a nation need be judged purely by whether inventions it made then are used now. Korea was not particularly great at science from the 16th-19th centuries, but it was great at science before and after, so I hardly see why we need fixate only on one period as a hallmark of Korea being somehow inappropriately scientific.
Korea led by Sejong and Seondeok was definitely scientific, so your criticism of Korea being picked as scientific doesn't seem applicable to their Civ V and VI incarnations. Similarly, Spain is portrayed as focusing on conquests in the New World and religion in Civ VI, but that wasn't true of them throughout all history. Nor was Arabia always scientifically advanced (after the Golden Age came a darker age). Nor was Scotland particularly scientific except in the 18th-19th century, but that forms their major civ bonus anyway.
Consider that Spain in Civ gets religious, gold, and religion-themed military bonuses under Philip II or Greece cultural and military bonuses under Pericles and Gorgo. Many of those bonuses tie to the leader and the nation *at that time* in history. Korea as portrayed in Civ VI is almost entirely medieval, from their theme song to their unique abilities, building and unit. So similar cohesiveness is found in their design revolving around Sejong or Seondeok. Also, you would get odd results if you had say a scientific US led by Washington (who was not known for his scientific contributions).
I also take this opportunity to note again that Korea, in its precarious position between China and Japan, was also very innovative in military technology. And they are as known for this as anything else now. Consider that in
Age of Empires II: The Conquerors expansion the Koreans had the weirdest unique units and were portrayed as "cunning". This is accurate. The hwacha and turtle ship were effective weapons used to devastating effect as a result of Korean theft of Chinese gunpowder secrets and innovative development of various rockets and cannons (like Choe Mu-son's gunpowder weapon development laboratory). See
https://en.m.wikipedia.org/wiki/Korean_cannon for more on that.
In Civ VI technological developments are tied to the military as much as to spaceships. Koreans had advanced cannon and gunpowder weapons that mowed down samurai and thrashed the Japanese navy despite being outnumbered. So Korean science bonuses in that sense are particularly accurate. IRL Korea had advanced cannons the Japanese generally lacked in the Imjin Wars, and the Koreans were able to beat them as a result, despite losing much land to veteran samurai.
Glad you enjoyed it! I appreciate your compliments. And yes, Korean innovations had quite an impact on 16th and 17th century Japan. I guess an ingame representation of this is Japanese samurai looting Korean science buildings. (And indeed there is the historical example of Ukita Hideie doing just that by looting Korean printing technology.)