I think I still like the third option out of all of those it is the simplest one as long as you understand that getting 100% is most of the time nearly impossible.
There could be three inputs that you use for each fire control in this instance... you set a "minimum" number of shots distributed for each incoming missiles a desired "minimum" hit chance per missile and the lastly a percent of how many shots out of the total assigned to that fire-control it is allowed to use (both minimum and maximum).
This give you a pretty good control over how the fire-control works with relatively little math needing to go on in your head aside from figuring out if you want to restrict the number of shots the fire-control may use.
This also should make it fairly simply to code... if you say that it has to shoot a minimum of "2" times per missile it will do that as first priority, then it will look at the minimum hit probability of there is any shots left. The minimum shots per missiles override both of the other settings, so if you set the fire-control to fire only 50% of it's shots that inly impact when it looks at the minimum hit chance. It should always respect minimum number of shots per missile regardless.
So.. I could set that I want to at least 2 shots on each missile and a minimum hit probability of 80% and that it may use 50/100% (minimum 50% and a max of 100%) of the weapons assigned.
The two shots are respected in combination with other fire-controls in the fleet... the fire control with then use at least half of the shots to reach the minimum hit probability. The fire-control will use at least half the shots even if the minimum to hit probability is reached and is allowed to fire all shots but will stop when to hit probability is reached. Shots above the minimum probability should just be evenly distributed among all missiles with no real regards with "to hit" probability anymore.
This way you can use both these methods... you can say you want to fire 5 shots on each missile and have a hit probability of 10%. Then you effectively are just using the first method in that instance.
I think that with these three simple settings you would mainly have to set it up with intuition rather than using a bunch of math. The minimum to hit probability is something you will only misunderstand once when you put 100% and all shots go into one missile. Also, what I'm trying to avoid here are that I have to tinker with the PD settings for each incoming missiles salvo. I want something that can most of the time be quite generic. Say "2" shots per missile 90% minimum hit probability and 75-100% usage of the fire control. This should then work in 90% of all cases most likely, especially if I have shields to cover any leakers.
My main concern regarding having a minimum hit chance is that it is not straightforward that setting this moderately high may cause a lot of shots to be absorbed by a small fraction of the incoming missiles. This problem is more prominent when the chance to hit of each shot is low.
A minor point is more of a personal preference. When facing a superior opponent where the PD shot is not abundant, perhaps engaging all missiles with a 50% leak chance for each is better than engaging 1/3 of the missiles with a 10% leak chance but leaving the other 2/3 unopposed. I.e., if the min hit chance limit is set, it may still have to be adjusted based on each opponent.