Did Japan actually use any production aircraft with inverted gull wings during WW2?
At least one - the Aichi B7A - although it saw little action, coming very late to the war.

The Aichi B7A Ryusei (愛知 流星艦上攻撃機 Aichi ryuusei-kanjou-kougeki-ki)
(&quot;Shooting Star&quot;, Allied reporting name &quot;Grace&quot;) was a large and
powerful carrier-borne torpedo-dive bomber produced by Aichi Kokuki KK
for the Imperial Japanese Navy Air Service during the Second World
War. Built in only small numbers and deprived of the aircraft carriers
it was intended to operate from, the type had little chance to
distinguish itself in combat before the war ended in August 1945. (source)

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The director of The Wind Rises Hayao Miyazaki may also be familiar with another Japanese gull-wing design, the Kawanishi E11K &quot;Laura&quot; flying-boat, which too saw service in WW2. However, its wing is not inverted.
 (source)