Why isn’t it ‘‘des’’ there? Which difference would that make?
Here “de” is used as in the form “de (undefined article) + epithet adjective + noun” which is the correct way of using de/des.
Note: The sentence is kind of weird, feels like the punctuation is wrong and should be more either :
Using de (undefined): Il y a de belles villes au Japon. Kyoto et Nara par exemple.
Try to understand it as: There are beautiful cities in Japan but I don’t know which ones. There are, that’s it. Oh Kyoto & Nara actually, just remembered.
or
Using des (defined): Il y a des belles villes au Japon comme Kyoto et Nara par exemple.
Try to understand it as: There are beautiful cities in Japan that I know/have in mind. And I’ll give you the examples of Kyoto & Nara.
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thanks a lot for the clarification! 
I arrived at this discussion by clicking on the link for the Spanish sentence “Lo vi”, which had as German translation “Ich lebe es.” I was hoping to find out how this could be an accurate translation. But this discussion seems to have nothing to do with the sentence I was questioning. Can someone help me understand (1) the Spanish sentence I questioned or (2) how that sentence connects with the discussion above?