Modifications to the game install folder will never be supported. We have an official way to create mods which has to be used.
Speaking of the sound mods specifically, there is Saved Games/DCS/Sounds/ folder - for test purposes/local modifications and Saved Games/DCS/Mods/resource/YourOwnModInASeparateFolder/ where you can have Textures, Sounds, whatever, in a separate folder, ready for sharing with others.
If you are missing any functionality and or documentation, and the only way to make a mod is to modify game files, please ask, we will consider supporting mods for that kind of things as well.
I'll try to post a more detailed info on sounds mods in a week or so.
Thanks.