1) the wav files will searched for in their search paths. In your case - in other modules.
SDEFs do not alter waves. They change the behavior of sound sources on how to use the waves. These are separate entities. A sound source uses the settings from its SDEF on how to play the referenced waves. The same wave can be used in 2 (or more) different sources to produce pretty different sounds, depending on the settings in their SDEFs.
2) Yes, these are tools to avoid restarting DCS while you are tweaking the files. The unloaded waves will be loaded as soon as they are required by the simulation. For example, when an object using these sounds is created.