Yes, without air protection our subs would have been dead meat when our DDs attacked them.
Actually, any impressions that there are too many aircraft is strictly an effect of time compression. There are not too many aircraft. I am presently in a career early in the war with an S-Boat out of Manila and they Surabaya when the air was lousy with airplanes. I have no radar. I still am using my yo-yo strategy, even with optical lookouts only with perfect success. My batteries are at full charge except when I am engaging shipping, I stay submerged for about 10 minutes during the three or four air attacks per day and I'm happy as can be.
Now, more confidently than ever, I can say that there are not too many aircraft in SH4, whether stock, TMO, RFB or any combination with RSRD. They can be dealt with. They are not a hazard.
By the way, I am using TMO without RSRD, and with a no radar sugar boat, the worst possible configuration for "excess" air attacks.
Time to bone up on your tactics! See the Sub Skipper's Bag of Tricks thread for pointers. If you don't have radar I'd keep time compression at or below 1024. I usually am running 512 in high air traffic areas.
