Espen, I think whales being migratory or at least moving mammals, defeats any sovereign rights issues of any NE Atlantic countries. Minkes migrate to where the food is and I doubt they want to carry EU (or Australian
) passports for fear of being hunted 
To say any whale that comes within 12 nautical miles of Norway is thus a sovereign issue is a good legal argument. However, I doubt the Norwegian whalers stop right at the 12 nm mark when chasing a whale. The population was estimated between 65-117k (mathematical estimates), so taking 1200 (2010 Norway quota) will be from 0.7-1.7% of the population. There is no data on how many whales are taken outside the territorial water mark.
However, when the Japanese do the same with pilot whales and dolphins "on their own shores", as the Faroese do, a movie is made about their savagery and lack of humanity. I don't think the criticism and general outrage is proportionate at all.
I believe the Japanese also hunt their quota of Sperm and Sei whales around their waters (including since they are right on the continental shelf and have access to the populations of Sperms around the islands). Moreover, the population estimate of the Sperm whale in the North Western Pacific is over 100k, of which the Japanese openly hunt about 50-100 a year. They only go for the Minkes in the Antarctic, where the population is even more robust (600k or more I believe) and can handle the 900 whales the Japanese claim to take every year. A study released this year shows the minkes are getting closer to pre whaling numbers.
You are absolutely right it is the overfishing of the ocean that is the biggest issue in marine conservation. In fact, the Japanese have argued that whales (some of them are now 1% of their pre19th century population) are competitors for fish, and thus need to be regulated, an argument many fishermen will support, whether the science is there or not.