If your file list is sorted alphabetically, it's the "periscope_UpDown.wav" file that does it. If you don't have the file, that would be strange, but explain the "silence" of the periscope in your game... As for the SH.SDL file, it doesn't control all of the sounds of the game directly, so you won't find all of the listings there.
As for Int and Ext files, usually the only differences in the files are the volume level and EQ settings applied to the Ext files, so they sound muffled and farther away (usually, with the Anti-submarine net sound being very different...
). Usually, the Int file will be stereo, and the Ext file will be a "set" 3D mono file, but not always. The inconsistency of file handling in the game is one of several challenges of doing mods... It also makes it look like there was quite a bit of "shooting from the hip" used during production... just sayin'...