For example, are there any ancient Korean manuscripts that only lie in some library in Pyongyang (and they dont feel like sharing)? Or are there very important archeological sites? Or does South-Korea pretty much own all the interesting stuff?
There's a large film archive for one thing. This is actually important to the South because many films from there have been lost due to neglect, for instance The Housemaid was only recently rediscovered in a print with Spanish subtitles that someone found overseas.
There have been instances in recent history where North and South Korea have loaned each other artifacts to better their relationship.
One thing that comes to mind right away in the statue of Wang Kon that was on loan in the National Museum of Korea years ago. Kaesong, the former capital of Koryo is in North Korea and therefore NK has considerably more historical objects pertaining to Koryo (while SK has more relating to Chosun).
After the division the North took most of Korea's prominent historians so for a few decades after the war, NK was even ahead of SK in terms of historical research.
There are also plenty of archeological sites in NK.
By no means does South Korea have most of Korea's historical documents.