A couple things I see right off that might be problematic, but which may have nothing to do with the hydrophone issue:
If you are using the M.E.P. environment mod, you don't need GWX 16k Atmo enabled as this would be redundant at best. The M.E.P. mod provides its own "extended atmosphere" and the GWX 16k Atmo should be disabled before enabling M.E.P. to avoid any possible conflicts. It's possible that the latter simply overwrites everything the former did, but I'm not sure.
Second, FM_NewInterior and LifeBoats&Debris both overwrite the same .sdl file with their own versions; you will lose the unique audio effects provided by whichever one is enabled first if you have not manually edited the relevant .sdl file from the second one to make it compatible with both. There was also a compatibility "fix" that worked for these two mods if you wanted to use both at the same time, done by Aces if I remember correctly. There should be a thread or threads on his various compatibility fixes in this forum somewhere.
Also, FM_NewInterior overwrites files which would already have been overwritten by GWX Integrated Orders, meaning that unless you manually edited those files to work with both mods, you've compromised the functionality of Integrated Orders.
Plus I think the GWX Open Hatch mod is probably unnecessary if you are using FM_NewInterior as there is an "open hatch" function built into the latter.
Again, I don't know if any of these redundancies and possible conflicts is causing the loss of your hydrophone. Since it seems to be an audio issue though I would look at the mods that affect in-game sound first.
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