Disconnect the water alarms, if wiring is allowed in your server. I don't like water alarms either, it's usually fairly obvious when there's a flood and I don't care about 1inch of water. If you just don't want the annoying sounds then replace the alarm with a flashing light (may need to build a flasher circuit).

Your electrical engineer is perfectly capable of "modding" the alarm in the submarine itself, ingame, in order to adjust it for his auditory needs. This includes, removing it altogether with a wrench, or adjusting the circuit so it doesn't change state easily.

A mod would be "i like the alarm but not the sound", so if you want a new sound this is possible. Doesn't seem like it's the case.

If your one crewman doesn't like the sound then they should be able to replace the actual sound file on their local installation of Barotrauma - it should be here:
C:\Program Files (x86)\Steam\steamapps\common\Barotrauma\Content\Items
Called AlarmBuzzerLoop.ogg

They would need to replace the audio file with something else (converted to the .ogg file format), maybe an annoying toilet dripping sound or whatever. No mod required, and it would only affect their own experience when playing the game. Of course, the next time Steam updates the game it would probably be overwritten so the file would need to be overwritten again manually. A mod could probably achieve the same thing without this need but I wouldn't know where to start with sound mods.