Of course smaller ships will usually have smaller computers, and ships computer capability can be degraded by combat (in most versions of the rules), so Gunnery skill will be more useful on smaller and combat damaged ships.
It seems to me that Gunnery skill models a reality in which Merchant ships need good gunners more than Naval ships do, because the Naval ships have such good computers.
It reminds me of how Thorby Baslim went from a firecontrolman on the merchant ship Sisu, to a gunnery crewman on the the Hegemonic Naval ship in Heinlein's 'Citizen of the Galaxy.'
http://books.google.com/books? id=wksN1qnkooAC&pg=PA196&lpg=PA196&dq=%22get+a+hit +with+that+junk%22&source=bl&ots=zx17CNEctU&sig=oG NjKn24P5QOZuRfdXGaXJEnyD8&hl=en&sa=X&ei=DY9tT6enGM fjiALfoMSxBQ&ved=0CCoQ6AEwAA#v=onepage&q=%22get%20 a%20hit%20with%20that%20junk%22&f=false