Class: Class sounds are played by a thing's soundclass (*.snd). These flags act like Thing sounds, but are much different. PlaySoundClass() can be used to play these sounds.
Position: Position sounds are played by Cog with PlaySoundPos().
Local: Local sounds are played by Cog with PlaySoundLocal(). Unlike Thing and Position sounds, Local sounds have no origin. Therefore they can be heard from anywhere in the level at the same volume.
Global: Global sounds are the same as Local sounds except that they are played on all computers in a multiplayer game. Hence the "local" and "global" designations.
There is no way with Cog to access a sound's flags ingame, but doubtless the engine can. So perhaps some of the unknown flags are used by the engine alone for the purpose of playing the sound. Also, some of the unknown Sound Flags (such as 0x2) may affect the CD music. But JK does have problems changing the music's volume on some systems, so it is possible that some of the unknown flags will work only on some systems.