If you are close to target ship, for example 3 km you should be able to see it with periscope or if you are on surface you can see it very clear with binoculars and also on nav map. But if you are very far away, for example 50 km when target appears on nav map, you should reed this threads in links below to learn how to intercep target, but I think you already cnow that.
http://www.subsim.com/radioroom/showthread.php?t=88961
http://www.subsim.com/radioroom/showthread.php?t=88922
Well if it is some bug in your game, someone who had the same problem in this forum will reply with some suggestions how you can fix it, or you can search for answers on google and find out if someone had the same problem with SH3 like you hawe with wanishing targets and find solution for that problem.
