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Japanese night air defense was nothing like that which existed over Germany during 1942 to 1945. Otherwise U.S. heavy bomber barons would have made different decisions in the Pacific.
There were several Japanese pilots and units that did well against the B-29, here's a few notable pilots:
Lt. Hannoshin Nishio, 2nd Chutai/4th Sentai flying the KI-45 - 5 confirmed
Capt. Yoshio Yoshida, 3rd Chutai/70th Sentai flying the KI-84 - 6 confirmed, 1 probable
M/Sgt. Isamu Sasaki, Army Test Center, Fussa Airfield flying the KI-84 - 6 confirmed (3 in one night, 25 May 1945), 3 probable
2nd Lt. Makoto Ogawa, 3rd Chutai/70th Sentai flying the ki-44-II - 7 confirmed
WO Sadamitsu Kimura, 2nd Chutai/4th Sentai flying the KI-45 (modified with two 70° mounted Ho-5 20mm) - 8 confirmed
Capt. Fujitaro Ito, 3rd Chutai/5th Sentai flying the KI-45/KI-100 - 9 confirmed
The max speed for the B-29 is 357mph (574kph) but this is an optimum speed. Fully loaded and they'll be doing less.
KI-44-II max speed: 376mph (605kph)
KI-45 max speed: 336mph (540kph)
KI-84 max speed: 427mph (687kph)
KI-100 max speed: 360mph (580kph)
These pilots were catching the B-29s inbound, which will be travelling slower than thier maximum possible speed. Many of the pilots were already at altitude waiting, so they dove in for the attack.
You'll notice that WO Kimura was flying a "slower" twin-engined aircraft (KI-45) with successful results, because he was catching the B-29s fully loaded inbound. Well, he also had a Japanese version of "Schrage Musik"...that really helped.
Japanese fighters were banned to fly to save their limited fuel.
They were only waiting for the allies landing on the Japanese coasts.
Gen. Lemay knew it very well.
He was a genius of war.
There were several Japanese pilots and units that did well against the B-29, here's a few notable pilots:
Lt. Hannoshin Nishio, 2nd Chutai/4th Sentai flying the KI-45 - 5 confirmed
Capt. Yoshio Yoshida, 3rd Chutai/70th Sentai flying the KI-84 - 6 confirmed, 1 probable
M/Sgt. Isamu Sasaki, Army Test Center, Fussa Airfield flying the KI-84 - 6 confirmed (3 in one night, 25 May 1945), 3 probable
2nd Lt. Makoto Ogawa, 3rd Chutai/70th Sentai flying the ki-44-II - 7 confirmed
WO Sadamitsu Kimura, 2nd Chutai/4th Sentai flying the KI-45 (modified with two 70° mounted Ho-5 20mm) - 8 confirmed
Capt. Fujitaro Ito, 3rd Chutai/5th Sentai flying the KI-45/KI-100 - 9 confirmed
I doubt that Allied intelligence would know that - particularly in light of the Kamikaze attacks at Okinawa. Also night fighter attacks would be a lesser force than a day attack and much lower altitude so fuel consumption would be less for night defense.