The compartment targeting mode has been disabled in GWX. More accurately, it was broken inadvertently, but the Grey Wolves team was very happy that it was and have stated that they would have broken it intentionally if they had thought of it. This is because there was a built-in "cheat", that if you clicked on one of those little boxes, a hit resulted in a guaranteed kill. If you just used them as a reference and aimed the torpedo yourself (either by unlocking and autoaiming with the crosshair or doing the full manual targeting routine) there was a certain percentage chance of a critical hit, assuming you hit it at all, but it was only a chance, not guaranteed. As a result, trying to click on the little boxes in GWX gives very unpredictable results, usually bad.
You can still use the unlock and aim with the crosshairs method mentioned above. The critical areas are still in the game. Note, however, that the boxes may or may not accurately show their location. The new GWX ships never had their boxes accurately placed (designers just copied the boxes from old ships over to the new ones) and since GWX changed the compartments around on the original ships, the boxes may or may not be accurate on those as well (though generally they are).
With that caveat in mind, here is a link to a chart showing the critical areas from the original SH3:
http://files.filefront.com/shipchart.../fileinfo.html
Green = Rudder
Blue = Keel
Pink = Ammo Bunker
Yellow = Engine Room
Orange = Fuel Bunker
Information in BOLD text is the ship's draft.
There is no such chart for GWX, but you can get good information from these two threads, discussing the best locations to target on ships.
http://www.subsim.com/radioroom/showthread.php?t=104045
http://www.subsim.com/radioroom/showthread.php?t=103928
Other threads have discussed best locations as well, just use the search function to find them.