If you install the GWX supermod over your game, you will no longer see colored icons on the map at all, no matter how close to a ship you get. The icons on the map will all be (and stay) the same color no matter where a ship is from. You'll need to ID every ship yourself by getting close enough to see its flags/markings/etc. from the bridge or the periscope.
But you can get the color-coding back after installing GWX by downloading and enabling the Contact Color mod. You can find it here at Subsim:
http://www.subsim.com/radioroom/down...?do=file&id=33
or at Jimbuna's Filefront page, there's a link to that in his sig.