You know, I'll bet the real skippers complained about too many planes too. But they didn't have the option of nerfing the enemy with a fortuitous mod to wussify their environment.
Yes, it's possible with RSRD to circumnavigate the Philippine Islands in late 1941, when they were under almost complete control of the Japanese without encountering a single airplane. Considering that on your way out to sea you just watched a movie about how the British moved their battleships out to interdict the Japanese invasion of Singapore and they were promptly sunk by swarming Japanese aircraft, how are you to defend such a thing? I doubt that a submarine could remain surfaced for more than an hour in that vicinity at that time. I've been on the surface continuously for four days except for sonar sweeps!
Fact: the air was FULL of unopposed Japanese aircraft.
Fact: they sank many valuable American and British naval ships, including some submarines. These included ships that could well defend themselves.
Fact: you complain that the game reflects that reality.
Have you considered that time compression makes the frequency of air attacks seem many times more frequent than they are? Have you actually logged times of air attacks in 12 hours in the game and compared them with WWII sub logs made at the same time in the war and in similar waters?
The issue isn't whether you can or can not choose to play the game any way you want. Of course you can. You can download my slightly subnuclear Mark 14 and incinerate any ship in the game with a hit to the rudder (it's a lot of fun!), but don't make claims of "too many airplanes" and "too few ships" without doing the extensive research on planes that the developers did or the incredible research on Japanese shipping that Lurker did. Go make the claim of not enough Japanese ships the RSRD thread and see how Lurker will drop reams of evidence on top of you. I dare you!

As a matter of fact, it would be a fun discussion and I urge you to do exactly that. I'll bet you will learn a lot in a hurry. And so will a lot of other people who would never ask the question, so you would be helping lots of people.
Learning is one of the valuable things that happen when you choose play a simulation over an arcade game.