To find out how to disable automatic ship recognition, go here.
http://www.communitymanuals.com/shii...ip_Recognition
On another note, if you have the time and want to invest some of it in learning more about the game, that link I gave you has all kinds of good info on this game. You can read it all in about 2 hours, and you'll learn a ton about most aspects of the game.
P.S. If you have manual targetting disabled, I'm pretty sure the target will be identified automatically even if you follow the instructions in the link I gave you. Since for me it's hard to start playing a game on easy settings and then make it harder later on, I just started out with all realism options on except for external cam and the stealth meter, that way I don't miss the auto-targetting since I've always done it manually. Manual targetting seems real tough at first, but once you get used to it you find easier ways of doing it that don't hurt your head so much.