I'm not so sure about that. These ships are not supposed to get into dog-fights - they are more like naval vessels than jet fighters. And even for the modern air superiority jet, dog-fights are rare. The new Euro fighter, for example, was originally designed without a gun (just missile mountings) because it was felt that guns are irrelevant unless you're going to be strafing ground targets. Even on the ground - with tanks - it's mainly about weapon range. Tanks don't drive around trying to get into each other's blind spots or hit the weakest part of the armour. The Abrams beats the T72 cos it can shoot twice as far, is all.
And especially in air-to-air combat these days it's all about your weapon systems, not the platform as such. If your missiles fly farther, faster and more accurately than the other guy's, you will win. It's as simple as that. The US Phoenix missile, for example, can kill its target from 80-100 miles away. Other missiles can't. The USAF wins.
Same with naval vessels, and it would be the same with starships. All this talk of maneouvering to get into position sounds like crap to me. The guy with the biggest, highest firing rate, most accurate guns (or whatever) that can reach the farthest would win every time.
So I don't think 3D would really do anything from a tactical perspective. And it would make controlling things a hell of a lot more complex.