Besides subs tend to stay close to surface. Correct me if i'm wrong.
When fighting, yes; otherwise, they might go relatively deep but are still close in absolute terms.
Indeed. I once had to explain to someone why thier space combat system didn't work. The gist of it was that combat takes place at a maximum range of one light-second. (300000km ish). It takes 1 second for light to travel between you and an enemy target at that range. So when you see a target you are actually seeing it where it was 1 second earlier. A laser weapon will take one second to reach the target, so there is a two second gap between when you fire the laser at an enemy based on where they WERE and when your laser actually reaches that spot.
Which is actually almost impossible to screw up, particularly considering the power of the computers they're using. You don't just see where they were a second ago, you've been watching them move for a while now. You know their velocity and distance (and two seconds is not a lot of time for the target to change course), so really any monkey should be able to shoot a bit ahead of where the ship is seen.
You also seem to assume that humans/Vasari will be aiming. In that time period, the absolute most that an organic is going to be doing is designating targets. If they haven't yet figured out to let the computer decide when and where to shoot, they deserve to lose the war.