For the same reason AMS is served by an Asian airline from 10 out of 11 largest Asian airports, including by non-Skyteam airlines like SQ, BR and CX?
Be realistic :
Japan is not Singapore, not Hong-Kong, not Taiwan : it is one of Asia's two long-standing economic giants.
With 126.8 million high purchasing power citizens, no less :
not 5.6, not 7.4, not 24 millions respectively. With 51,5 million, SKorea is some 40% of Japan.
Thus, if either Japanese airlines saw commercial potential & wanted access to AMS, they'd be flying there long ago. Period.
Let's not forget that SQ and CX can get transit traffic, i.e. AMS-SIN-SE Asia (i.e. Indonesia or backtrack to Malaysia)/AusNZ, or for CX, AMS-HKG-AusNZ/Mainland China (Although less so the latter case as KL along with Skyteam are very strong in mainland PRC).
Taiwan is an oddball case - it's more or less bilateral (Netherlands being one of the first few countries in Europe (IIRC...I can be totally wrong) that allow non-stop from Taiwan, this was back in 1980s or so) and historical reason.
AMS->Japan is pure O&D, while Japan->AMS is largely transit traffic with a some Japanese tourism traffic to Netherlands thrown in. Thus, KL greatly benefit from the transit traffic direction.
ares to secondary Japan appear to be constantly higher than to secondary China, so I'd be somewhat surprised if they cut from those. Although the additional overnight frequencies to KIX could be a candidate.
Now if we want to think out of the box, and I stress that this is pure speculation and not likely to happen, AY does have a history with flying the polar route to Tokyo, bypassing Soviet airspace. The route would be around 3000km longer than the Siberian one, and take a few more hours to fly. Now, having an overnight flight does usually increase J demand. So, let's say that if AY would be desperate enough to send their A350s somewhere, it would be funny to see them resurrecting the polar route by sending an A350 each night for a red-eye on each direction.
Obviously that would severely impact the whole idea of flying the Northern shortcut etc among other hindrances, but it's still a fun idea.
Tokyo dominates Japan but is not the end all for Japan. For instance, before BA restarted KIX-LHR, most pax flew KIX-HEL-LHR (via AY) or KIX-AMS-LHR (via KL). Those are traffic that AY looks to capture (alongside boosting tourism to Finland by Japanese) - it's the exact same reason why AY fly to those secondary Chinese cities and had pushed to fly to PUS (in South Korea) for years.
JL codeshares with AZ too if I'm not mistaken.
They don't. AZ's flight are listed on ANA's timetable but not JAL's.