That is part of the 'realism'. If you pass the cursor around the area where the ships should be, you should see dotted circles. If you click on one it should give you very limited information, such as "unknown".
If you identify the ship with the UZO or periscope it will show up on the Attack (TDC) Map. Click on it and it will now appear on the Nav Map.
The idea is to have no more information than you would in reality. The Attack Map is for attacking the enemy, one at a time. The Nav Map is for navigating. Of course, there are people trying to make it even worse, and I love them for it:
http://www.subsim.com/radioroom/showthread.php?t=93937