score:16
Yes, you're overthinking. The name of the game in North Korea is brinksmanship: they push the envelope to extract concessions, but are not stupid enough to commit an actual act of war, like shooting down a passenger airplane.
Also, North Korea does not test anti-aircraft missiles, but ballistic missiles aimed at specific targets on the ground. These fly high and far (>1000 km altitude is not uncommon), way beyond the cruising altitude of passenger airplanes (10 km).
Finally, not only do Japanese aircraft do not enter North Korean airspace, but routes to SE Asia don't fly near the country. Here's Tokyo to Bangkok (map courtesy gcmap.com), which doesn't even cross South Korea (the peninsula at the top right).