Nice story.
Subnet modelling and ambient sound modelling was not a feature of SHIII. The only ambient hydrophones sound is the lapping of waves etc. No whales, no subnet chains clanking even in heavy weather.
I'm not sure what the deepest subnet is as I've never tried to infiltrate Curacao, but you can go over the subnet at about 8-9m as they float at around 10m. This WILL expose your conning tower but if you can porpoise fast enough and quiet enough and out of sight of the patrols you can do it. See my harbour Infiltration manual:
http://www.subsim.com/radioroom/showthread.php?t=96843
You might have problems though in heavy weather as you will likely get hammered against the top of the net.