Both situations - damage from surface detonations and getting decent sonar from aircraft, are relatively easy fixes - simply limit AOE range when a projectile hits water, and you'll get a rather realistic simulation of the natural mechanic without taking ground fire completely out of the picture - in about 3 lines of code.
As for getting sonar from aircraft - it's actually already there - but - due to the elevation of the aircraft that have it - and the range of the sonar they carry - it actually doesn't penetrate a whole lot of water area. Either the sonar range would have to be adjusted for the elevation, or the sonar would have to emit from an invisible bone that hangs well below the aircraft. The proper solution would be to create an intel entity which drops from the aircraft, every few seconds, and if it lands in water, becomes a short term sonar buoy. The code for that too, is already in the game - it's used in the Aeon Eye of Rhianne, which creates a vision entity. This would be an adaptation of that.