Most of today's manufacturers have some connection to WW II, but Subaru, Mitsubishi Motors, and above all Nissan would be the current names most directly associated with major roles in Japanese defense production and policy during WW II.
Subaru is a descendant of the Nakajima Aircraft Company of the WW II era Nakajima Aircraft Company, contintinuing after WWII as Fuji Heavy Industries, now Subaru. Mitsubishi Motors is part of the Mitsubishi Group, but the defense part of that group Mitsubishi Heavy Industries doesn't make cars.
Nissan had a factory in Manchuria, and its founder Aikawa Yoshisuke was the head of the Manchuria Industrial Development Corporation, a major player in Imperial Japan's industrial plans. Aikawa is a bit of a contradictory figure. He was close to American industry and finance before the war, and was part of attempts to prevent war, but his actions in Manchuria left him perceived as one of the more notable villains. He was arrested after WW II and charged with war crimes, though later released. The Nissan zaibatsu was dissolved, but you can trace today's Nissan back to the pre-war zaibatsu.
Toyota was a relatively minor manufacturer of light trucks during the War, what later became Honda was a small manufacturer of parts for Toyota. Companies now known as Isuzu and Mazda were similar, manufacturers of light trucks during the War; Mazda also manufactured some of the Type 99 rifles.
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