There's a point at which the time spent boarding becomes too great considering the time in the air. The A380 is a large plane, and you really need 3 jetways to board it in any amount of reasonable time. The mentioned routes are mostly operated by 767s, 787s, 777s, or 330s. The 767 is the perfect plane for the route, and the 330 isn't half bad. TPE-HKG is another example of one of these super busy short routes.

Japan is usually a Boeing backyard.

Case in point with JAL (not sure if they fly the routes you talked about but it's as good as an example): https://www.jal.com/en/outline/aircraft.html

231 aircrafts, not a single Airbus.

yes if you look at busiest routes you will find the top few dominated by short domestic routes less than 1000-1500 km. you run a short range plane like the a320 or the 737 and fly the route 100s of times a day. it's much cheaper than running a few a380s.

the a380s are almost only used for long range flights with 1 or 2 flights a day: sydney-dubai-heathrow, singapore-london, singapore-frankfurt-new york etc.

And smaller planes flying more frequently yield a better experience for the customer, too. There's more flight times to choose from, boarding doesn't take as long, and there's many more jetways available for smaller planes at airports.

ANA operates the 777 on those routes, hell I've even seen it flown on Tokyo-Hiroshima and it was full. A case could certainly be made for the A380 on Tokyo-Osaka.

You would need 15 doors to fill them fast enough.