Yup, a lot of these bonuses make no sense. The best/worst one I saw on the first page was the Spanish naval bonus. Sure, they built the Armada, but does Firaxis remember what actually happened to the Armada? It was pretty soundly defeated. And the Spanish didn't prove remotely competent naval combatants in later wars with England either.
Then we have China's no anarchy bonus (few major powers have had MORE internal dissension/anarchy in the 20th century than China, once you combine the warlord period of the early 20th with the revolution/civil war of the mid 20th).
I'm sure there are more - plus, as a previous commentator pointed out, plenty of obvious historical bonuses that are missing - but I just skimmed the thing.