Couple items, in the OPTIONS, SOUND menu there's a slider upper left that controls the number of 3D sound channels, minimum 1 channel max 4 channels. If that slider is all the way left or your sound card isn't capable of processing 4 channels you only hear one sound at a time, although because of the speed modern computers operate it might sound like you're hearing multiple sounds simultaneously. Item 2, 4 sound channels will drop sounds in SH4 when there's a lot of action and more than 4 sounds at a time.
I don't think any mod is to blame for the OP's problem, I'm playing with no megamods and sometimes I hear the tube outer door opening sound, sometimes not. The whole sound system is a mess IMO, voice saying "rudder! rudder!" when you order rudder amidships, I just turned the voices off in the OPTIONS, SOUND menu because it's more immersive without idiots constantly saying idiotic things. The "PASSING THERMAL LAYER!" loud stage whisper is apparently not in the voices, and all too frequently gets caught in a sound loop even when you're on the surface, so I just changed the WAV file so it's quiet bubbles that I can ignore.
I have no idea what processes which sounds get dropped and which have priority when there are more than the game can handle, but if that can be found it might be worth looking into.
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