This is the final solution I ended up with: metal case + old 939 stock cooler. . I was not totally satisfied by the metal case only, probably also because I keep the nanopi in a closed environment with no air circulation. Previously I tried also the heatsink with the small fan, but it's rather noisy and doesn't help a lot if you still use the yellow case.
I'm experiencing similar temperatures with the yellow case. I checked the board and the thermal pad adheres well to the soc and the heatsink. I think the only solution indeed is the aluminium case. I ordered one few days ago, but still it hasn't arrived yet so cannot say anything about its performance.