I agree that the effect of the gunnery skill check should affect the effectiveness of an attack as it does with personal combat and barrage attacks. This would make space combat considerably more deadly for no-armor vessels (most PC ships). A highly skilled gunner could make a sandcaster a deadly weapon.
Well, IDK about your players, but most ships mine have had (Scout, Seeker, Free/far traders) have some armor. In fact, the classic ships without it in MgT are the fat trader, lab ship and corsair...
If I were to introduce this as a house rule I think I would have to limit it. Perhaps allowing the attacking vessel to ignore armor points up to the effect of the skill check. That is, skill would allow the attacker to circumvent armor, but damage would still be governed largely by the power of your weapons.
Still thinking about this but good fodder to chew on.
IMHO, adding the effect to the damage roll is a good way to reflect a good hit and discriminate it from a marginal one, and, as said, quite coherent with personal combat, so, again IMHO, if applied, it should be regardless armor.
See that in the case of missiles, the effecdt that would aply would be the one for the final rol (without direct effect from the gunner, as it's an independnet roll).
A good gunner (let's say skill level 3) with good computer support could obtain, by rolling boxes, about effect 10 hit or more, meaning what in many games would be a critical hit, and able to damage even a battleship (though probably it will hardly feel it, as it would be a scratch).