Now I describe how to delete not necessary water nodes via Silent3ditor [S3D]:
http://sh4.skwas.net/downloads.aspx.
My skin has little less water holes. If You using water stream mod and use my skin, then You can see durning the game which water streams are not necessary.
Yes we can delete not necessary water nodes in S3D, and this operation is realy not so difficult.
Copy Your orginal files before changes
I use a
file 
Data/Submarine/NSS_Uboat7c--->
NSS_Uboat7c DAT file for example from this version of the water streams:
Water_Stream_for_Uboats_V4
We open
NSS_Uboat7c DAT in the S3D and we see something like this, and we click at the red areas/markers follow the numbers:
After this we clicking 2x fast via left mouse on the [ everything is on the next picture]:
The markered nodes in the right window on the 3D model view we must delete. This is example. Maybe You have a different version of water streams.
...in a few moments I will write a second part of this short tutorial