You can ignore the subs, but if Japan scrambles a fighter the subs can fight in the sea battle.
Rules clarification on scrambleing vs an amphibious assault
Okay so situation. Germany has 6 transports and a destroyer in SZ112 they move them into an empty sz110 for an amphibious assault on London. UK can scramble 3 fighters to fight the German sea units. Can Germany fly aircraft into sz110 in there declare attacks phase in order to cover their transports?
Yes. Germany can fly as many planes as they want, that can make it with a legal landing zone, into the Sea Zone during the Combat Move Phase.