If you use overdrive effects you're max speed is doubled and push effects can make your warhead reach these speeds, I've found that in most situations this will catch even some smaller targets. I also put shields on my warhead so that they can't be shot down before they've actually hit the target, and since their so fast they are typically hard to hit, even on default max overdrive speed 100, and impossible to target on 200.
Additionally you will want to put radar jammers on your warheads to stop missiles, ai ships and turrets from locking on to them, making cannons the only semi effective way to deal with warheads.
Unfortunately, warheads are still all but useless due to their strange damage scaling with shields, but if one is able to bring down shields warheads will eat through even adv hull, leaving a sizable chunk in the ship they've been fired at, roughly 8 radius hole was left by a warhead I launched at a chunk of yellow adv hull, and I shudder to think what kind of damage even larger warheads could cause.