There are other tricks to see into the fog of war as well, though I can't remember them off hand.
I disagree that it is an issue.
Let's say the normal viewport is optical and the C2 window is radar. It makes sense they wouldn't always overlap.
From a gameplay perspective, the z-targeting thing is also fine, because you can only lock onto a ship that is in range, and if you switch targets you lose the lock.
Perhaps simply formalize it as a lock, and then, if it is too jarring from a fairness standpoint - I can lance it and it can't lance me back - give ships the ability to shake locks. An ECCM pulse glitches your screen for a split second, and that's that.
Crap, I bet ECCM would be crazy fun when designed by this team.