I've acquired the Annihilator Beam weapon module in one of my play. Supposedly, the weapon fires once every phase, with a cooldown of precisely 40s.

However, the module tooltip in ship design screen shows a 47s cooldown all the time. I've looked into the source files (SimulationDescriptors[ModuleDLC1]) to confirm, and see that the cooldown is in fact 40s. I've yet to find any other updates that modify the beam cooldown, or any specific tooltip change that adds the 7 s to the shown cooldown. 

Then why does the tooltip show 47s instead of 40s? Anyone has any idea if this is intentional, or what cause this? 

Correct me if I'm wrong, but here is what I've found so far: 

The Annihilator Beam weapon definition lists both the basic beam weapon group modifier and the specific Annihilator beam weapon modifier. Now, this is basic for every other weapon in the game, the weapon group modifier dictates common things like cooldown, accuracy at different ranges, firing duration, preparation duration, ... while the specific weapon modifier adds onto it the damage, crew kill, or special effects like splash damage, increase opponent weapon's cooldown, ... This also explains why the turret EMP missile also has the same range effectiveness as the torpedo weapon group. The EMP weapon cooldown is also dictated as 150% that of normal torpedo weapon, using Percent operation instead of Addition as normal. 

Most of these modifications are made via the Addition operation. If the weapon group modifier and the specific weapon modifier both target the same property (be it damage per shot, cooldown, crew kill, ... ), they most likely add up. Normally a beam weapon has 6.8s cooldown (rounded to 7s in tooltip), and the Annihilator beam adds 40s, to 46.8s in total. Most likely, someone who was in charge of coding the DLC1 modules modifier didn't make up for the fact that beam weapon has 6.8s inherent cooldown. Editting this to 33.2s solves the problem, and the Annihilator beam has 40s cooldown as intended. 

I also noticed a modifier called "Only fire once per phase" (paraphased) in the Annihilator beam definition, which it shares with the AOE nuke super weapon. However, I doubt it does anything but adding "This weapon fires once every phase" to the tooltip. 

Again, correct me if I'm wrong, and how do you think it works? 

Thanks for the file location of this -- I was going to ask {I'm modding the TargetingWeightBonus of a few weapons and modules here and there is why}.  Anyway, is a phase 40s?  I suspect the cooldown timer is just trying to match the actual time of a phase, so this being my guess to how it works.

A phase is 40s, there is a Modifier in the weapon definition of the Beam, called "WeaponFireOncePerPhase" or something like that. It doesn't change the cooldown, but only seems to add "This weapon fire once per phase" to the tooltips. The cooldown was changed manually, by adding more Cooldown to the beam-based weapon (which has ~7.5s cooldown).