Why were the Japanese so much better at night flying early in WWII?

Japanese planned to use night tactics on strategic level

Traditionally, large armies or fleets avoided night battles. Because of reduced visibility, it was difficult to control large formations, and night actions would devolve into series of confused skirmishes. Prior to WW2, night was favored by small units that could operate alone or in small groups, and relied on stealth (torpedo boats and submarines, zeppelins and night bombers targeting large areas, small bands of specially trained raiders etc ...)

However, night fighting had certain potential that was favored by Japanese. It allowed attacker to bypass certain strong defenses (fighter aircraft, long range artillery both on land and on sea) that would decimate his forces during daylight. It also reduced effectiveness of observers, thus increasing chance of surprise. Since Japan planned offensive wars to increase size of Empire, and since potential adversaries (US and Great Britain primarily) had advantage, both in treaties like Washington Naval Treaty and in real size of forces and in industrial might, night tactics were one of unorthodox ways of fighting that could mitigate that advantage.

To this end, both IJA and IJN, with their corresponding air services, planned and used night attacks in WW2. Without going into much detail, IJA used night attack in Singapore, Guadalcanal etc ... IJN also prepared themselves for night battles, using superior optics, long ranged torpedoes and of course training. Their biggest success at night came at Battle of Savo Island, shortly before US advantage at radar technology negated any Japanese advantage.

Now we come to the question of aerial warfare. Important difference between Japanese and Western air forces was that Japanese planned from the beginning to use their aerial power at night against same targets they would attack during the day. Japanese didn't plan to divert large forces for area bombing or night harassment. Instead, as this report claims :

At Night

The Japanese apparently feel that moonlight bombing operations are not materially different from the same thing by day. They generally precede their raids with the usual reconnaissance, fly in formation, and use the normal pattern-bombing procedure with light bombs

In a recent attack on a U.S. Navy surface force, Japanese medium bombers approached during darkness, in 2 formations of 12 planes each. One plane detached itself from the formation and flew parallel to the course of the ships on one side, for a distance of 5,000 yards. During this run, it dropped float flares at intervals of about 600 yards. The plane then flew about 5,000 yards across the course of our ships, to the front, and dropped a second line of flares at approximately the same intervals. Finally this plane dropped a red flare and a green flare abreast of the formation and outside of the parallel row of flares.

Japanese night torpedo bombers were potentially even more dangerous, as witnessed in Battle of Rennell Island, were they managed to sink one heavy cruiser. In fact, Admiral Nimitz claimed that from late 1943

The principal tactical problem confronting the carrier task force is defense against night aerial torpedo attacks. During December over 90 percent of all Japanese offensive aerial effort in the South and Central Pacific occurred at night.

In all this effort Japanese didn't use any special technology unknown to US. Instead, they first and foremost trained their bomber and torpedo aircraft crews in night navigation and instrumental landings. This may sound trivial today, but most of pilots (especially fighter pilots) during WW2 simply didn't posses these skills, as they were deemed to complicated and time consuming to learn (and the need for pilots was great). Japanese also used moonlight and preferred to attack in the nights with clear sky and full moon. Finally, they often sent dedicated planes to illuminate targets with flares before the main attack. None of this was revolutionary, but when combined and well trained it would enable Japanese pilots to have an edge in combat.