It's a small one, but one that matters.
I've noticed that all bombers firing non-guided payloads do not lead their target - they always fire head-on, at the position their target currently is at, instead of at where they're going. This matters less with a Khopesh, for example, but severely limits the usefulness of Piranhas and Flashes, which drop slow-moving bombs and prox charges. If the target is a light cruiser or less, chances are they will just nonchalantly dodge to the side and all that damage will just float lazily next to them, into nothingness. I swear, I've never been hit succesfully by a Piranha simply because of how easy those bombs are to dodge (at shoot down).
Now of course, I know it shouldn't be too easy for those bombs to hit - they do crazy damage. Nor do I claim bombers aiming ahead of the target will mean certain hits all the time. Still, I feel it's just something they should do. Even Perditions suffer from this, often firing an entire barrage that completely misses, just because their target is moving sideways. Cobra seems to be less affected, because it tends to fire its Reaper at shorter range, but still doesn't lead.
I pretty much always gravitate towards using homing torpedo and kinetic bombers, simply because of how reliable their are. Unlike the rest of the bombers, they are effective against any ship class, including frigates. Even Tridents are worth their cost, simply because you can count on their Atropos to hit their mark.
And just in case you're wondering: No - Wing Commander 3 does not affect bombers (at least it doesn't seem to). As far as I can tell, it only affects accuracy of fighters.