The Navigation Map sub icon is found in the Data\Submarine\NSS_
SUB NAME folders (each sub has the same icon, but they have a different file name for each sub) For example the Balao icon is found in Data\Submarine\NSS_Balao\NSS_Balao_shp.dds. The "NSS_
SUB NAME_shp.dds" file is what you're looking for.
The .dds image is only 32x128 in size. The sub icon is found in the
Alpha Channel of the .dds file. This means you need to have a special image viewer or paint app to work with and change the .dds image. A simple, yet effective app is the BXTBmp Bitmap Manipulator found
HERE. The BXTBmp allows you to work either in the main image or the Alpha Channel image and "saves" your work in the original .dds format.
To make a blank Alpha Channel (which is what you want to do if you wish to remove the sub icon from the Nav Map), use the menu tools of BXTBmp and click on "Alpha", then "Send Alpha to editor"
after you have the "NSS_
SUB NAME_shp.dds" loaded in the app. Once the Alpha Channel appears, you will need to color the icon with the same black background color the image has. Once the icon is erased, "save" the Alpha Channel image by using the File\Save menu keys. Exit the Alpha Channel editor, then use the File\Save menu keys
again to save the entire .dds image. The icon is removed for that particular sub. You'll need to do this with each sub, so copy and paste the new image file into each subs folder and change the specific name to match the sub your putting it in.
If you've done it right the Nav Map will not have a sub icon showing it's position.