DISCLAIMER: Please note my answers are based to the scenario described and limited to such situation. In any case you should assume my criticism on the single entry to be the rule. In the specific I do believe it is important to have both CIWS and some sort of beam weapons in larger scale conflicts and/or small skirmishes.
Couple of things:
1. Your "nice" ships should not have much if any CIWS at all. They are ok for civilian/commercial ships (cause it keeps them non-military). But one should not rely on them for true PD, especially alone. The mantra is LAYERED DEFENSE, AMM's, LR APD, MR APD, SR APD, and CIWS.
2. CIWS is 2 gauss cannon on a self-contained turret. So you having 8 meant 16 shots so killing 13/16 is pretty good. However, they are all considered under 1 FC, and in general their range is not enough to get one shot at a missile salvo.
Now if all those salvos came in the same 5 sec "tic" then they fired once in that "tic" and can't do anything more.
1. I disagree. CIWS for a commercial ship is good but you need more protection if there is only one ship (more on the second point). So the layered defence may work for them or big fleets when not all ships can waste tonnage on PD. I think CIWS is more than enough (I use sets of 4x4) in lower mid-tech.
2. You can stack CIWS. Yes, it was very good (bringing the conversation to my next point). The rules in aurora have changed so you can target as many salvos with a CIWS or a PD for instance. The final consideration is your tech VS the tech of your opponent. There are some fights you cannot win and some others that even if you have a better design you may lose because of poor design. And that is with or without CIWS or layered defence.
So.
Got one of my nice ships blown up by a hostile NPR. Want to minimize this from occurring in the future.
Analyzing my event log, I see that it appears that only one out of my eight CIWS fired upon the incoming enemy missiles which destroyed the ship. NPR was flagged as hostile. Enemy missiles were arranged in 3 salvos of 21 missiles each and 1 salvo of 7 missiles. My ship had zero fire controls and one active grav sensor.
My expectation was that all 8 of my CIWS would fire. It seems that only 1 of my CIWS fired and destroyed 13 missiles in 1 salvo. The rest don't appear to have done anything. UNLESS I am misunderstanding things and ALL of my CIWS fired and just have horrible accuracy. But based on how the even log reads, I would have expected one log entry for each CIWS in this case, but I only have one log entry for one CIWS.
Is this due to a lack of dedicated fire controls or grav sensors? Or am I misunderstanding CIWS targeting?
I think the reason you died was simple: 1 ship against enemy multiple ships and or too many batteries to face. If you had 4 destroyers or scouts all equipped with CIWS your enemy would have scattered the salvos between your ships rather than targeting only one. This would have made the salvos manageable for your CIWS (as you saw you could shot 13 just with one).
In my last game, my simple patrol of 1 leader destroyer and 4 missile destroyers all equipped with 5 launchers each and a magazine of 200 missiles could manage to hold off 7 NPR ships with tech just a bit below mine. There were salvos of 8 missiles per ship, probably 10 or 12 of them and not a single hit thanks to my CIWS 4x4 12,000km/s tracking. And that is a tier 3 CIWS, imagine at higher levels.
Now if you were fighting a bigger enemy (say 9 or 10 ships, one of which a carrier) then you would have been in serious trouble because a 2:1 ratio will be hard to manage only with CIWS.
Also if you were facing 24000km/s missiles you definitely would have required some PD to take advantage of the bonus in tracking and be more effective, then maybe calibre your CIWS to a 25,000km/s tracking for the future.
Bottom line, based on your description of the events, another battery of CIWS would suffice to get away of that fight and if you were approaching them, let's say with 3 ships, I wouldn't be worried too much unless they have other surprises waiting for you. Then it would be your call if said ships are meant to explore or to attack.