I am taking Matt's advice and re-reading rules to apply them just as they are, and not 'Read too much into them'.  I find the Anti-Drone trait rules are actually quite clear as written, so I do not have any questions now about how that works.  There are some ships statistics though that have raised a question in my mind regarding the trait:  The Orion ships.
My son and I are going to have a play test this week involving the Orions and also adding terrain for the first time.  My question revolves around the optional mounts and drones on Orion ships.  Let's take a Salvage Cruiser as an example.  It has a 4 drone weapon system, and two optional mounts.  Lets say I choose a drone for each optional mount.  If we use the simplest interpretation of the rules, when I nominate that ship to fire, I would nominate a target for all three separately (i.e. I could target all 3 at one ship or 1 each at 3 ships, etc.)  It would also mean that each of those attacks would have to be dealt with separately by any ship with Ant-Drone traits.  (Thus the post on this thread.)  So, taking our Salvage Cruiser shooting at a Klingon D6, the Orion declares that he fires the drones in order 1 AD, 1AD, 4 AD.  
First 1 AD attack:  The Klingon would roll 1d6 and no matter what, the attack is stopped, however, if a 1 is rolled then the system is out of ammo and the Anti-Drone has no effect on the next two 'waves'.  
Second 1 AD attack:  If ammo still exists, then the Klingon player rolls 1d6 and and no matter what, the attack is stopped, however, if a 1 is rolled then the system is out of ammo and the Anti-Drone has no effect on the next 'wave'.  
Last attack 4 AD:  If ammo still exists, the Klingon player rolls 4d6 and no matter what all 4 dice are stopped, but if any of the 4 come up as '1' then the system is out of ammo.
In other words, having 3 drone systems on a single ship gives the Anti-Drone equipped ship 3 chances to run out of ammo and the possibility of getting later weapon systems drones through.  This differs greatly from just grabbing 6 dice, all 6 AD are stopped, but there are 6 chances to roll a '1' and have the system run out of ammo.  
(Come to think of it, since these are different 'weapons' then any ship trying to evade the drones would have to make 3 opposed rolls:  Two for 1 AD each and one for 4 AD, correct? )
The example above (3 separate waves) is how I would apply the RAW.  Is that correct in the view of the author/Rules Masters??