Sure, why not?
There may not be a naval battle occurring immediately once the US Transport enters SZ6, since there are no Japanese combat ships in the water, however the Japanese Kamikazes and Fighters are protecting SZ6; thus they are able to act after the Combat Movement Phase is completed and before the Combat Phase begins.
Kamikazes cannot be used against transports or submarines so the transport may enter the “empty” SZ6 by itself in safety. However, upon entering SZ6 the Japanese Player now has the option to scramble to protect SZ6 and therefore the transports can now be attacked. There does not have to be a naval battle already in place for the planes to scramble; their scrambling itself creates the naval battle.
Axis and Allies Pacific 1940 Rulebook (2nd Edition)
Page 15 (Bold added by me)
Scrambling is a special movement that the defender can make at the end of this phase. It must be done after all of the attacker’s combat movements have been completed and all attacks have been declared. The attacker may not change any combat movements or attacks after the defender has scrambled.
A quick reaction team of no more than 3 defending fighters and/or tactical bombers (strategic bombers can’t scramble) located on each island or coastal territory that has an operative air base can be scrambled to defend against attacks in the sea zones adjacent to those territories. These air units can be scrambled to help friendly units in adjacent sea zones that have come under attack. They can also be scrambled to resist amphibious assaults from adjacent sea zones, whether or not the territory being assaulted is the territory containing the air base. They may defend against the enemy ships conducting the amphibious assault even if friendly ships are not present.
