Your ideas are definitely useful, I love hearing suggestions to improve the sim
Aircraft will definitely be in the game, both fixed wing and helicopters, as they have a unique and vital role in modern naval warfare. At first I'll probably add anti submarine aircraft and patrol aircraft like the P-3 Orion, Nimrod, IL-38 and Breuget Atlantic but many more will eventually be added, including carrier-based aircraft and helicopters. I'm not aware of any widely used submarine launched anti-air weapons so I don't think it will be possible for the player to engage hostile aircraft. But they will definitely pose a threat, and will make operating near enemy coastlines a lot more difficult.
Armed warships are not just a possibility, they're already in the next version and seem to be working pretty well! Currently there are destroyers with 5" cannons, frigates with anti-shipping missiles and cruisers with both. They fire at you if your submarine is surfaced within visual range, and I'm looking at the possibility of adding some kind of torpedo or ASROC for surface vessels to attack submerged submarines when they are detected on sonar.
Sound effects would be great but it's often difficult to find high quality free ones. That wiki link is very useful though and I'll definitely be using some of those alarm sounds.