It depends how you imagine things working. To go a very long way back, to the age of sail, RN ships of the line seldom outshot the French and Spanish by less than three to two, frequently as much as four to one, from basically identical ships, the only difference discipline, training, and willingness to fight- in other words, crew quality.
Even now, the very best SSN crew, say, can only make their equipment perform to it's limits. It is terrifyingly easy to do less than that, through stupidity or inaction to leave things undone or badly done, and get killed thereby.
I could make a case that CQ should modify the basic stats of the ship. A good engineering crew can get more power out of their engine plant resulting in higher speed and possibly more turns, a bad crew lose speed, lose agility, do shoddy damage control. A good gun crew shoots more accurately and serves their weapons more quickly, achieving the equivalent of extra AP rating, more AD, more range, additional traits- all of naval history shows that skill defeats incompetence, consistently and often against what seem to be heavy material odds. The difference between a CQ 2 and CQ 6 crew should be bigger than the difference between a Hermes and a Marathon.
On the other hand, don't hold your breath waiting for a neat, elegant system to model this.