Standoff Missile Tech. If you have faster speed than enemy ship,in real combat you would control the distance of your ship to the enemy if you had missiles with long range,you could utilize this to have an advantage.You could reflect this by giving a slight % damage increase to missiles or a lowering of ECM or antimissle effectiveness.Researching Standoff Missile Tech would unlock this increase.

Ship Tactics-Beam Tech. Beam weapons.Because energy disperses over a distance a beam weapon would be more effective close up.If your ship has faster speed than enemy ship,as in the above example you could close the distance thus making your beam weapons more effective.This would be reflected by a slight increase in beam weapon damage by a % modifier once Ship Tactics Beam were researched.
Would be fairly late in the tech tree and tied to medium to large hull sizes.

You would not get multiple percentage damage for speed differences >than1.