In Special Supplement 3 (I think it is, Missiles), the movement of missiles is supposed to duplicate the movement of ships. If a ship can only move in a single direction (toward or away) it makes the intercept solution simple for a player controlling a missile. With two dimensions, the intercept solution becomes more difficult and there is a better chance to evade or for an evading ship to force a missile overshoot or undershoot. The same for a pursuing ship - you don't head toward where the ship is, you head toward where the target is projected to be or at least such that you will have a vector that comes within a certain distance of the target - but for missiles with limited thrust turns available you certainly would want to be able to maneuver with two or three dimensions if you are evading, in my view, anyway.
Fundamentally, until you add the missiles or a world, all your 3 dimensional BS resolves down to one and ONLY one important factor: Range to target.
If missiles are seekers only, only the pursued's missiles matter, because The aggressor is going to follow the same basic course as the missiles. The target's missiles, however, can force a diversion of the aggressor.
And while the 360 degrees of diversion matter from a choice point, unless there's a planet or 3rd ship, which of those 360° you pick makes no difference to the missiles nor the target firing them defensively. The aggressor either reduces closure rate, or diverts weapons.
Note also, while it's theoretically possible to go after a higher thrust ship, unless you can disable them before their thrust overcomes your potentially higher initial inertia and/or weapons range, they can and will escape.
That you can maneuver in 3D really doesn't matter, since at the end of the firing cycle, you're either closer or further from the target.