Two key points of confusion:
- Tooltip specifies no duration, so presumably this upgrade is permanent.
- Tooltip just says it affects "all ships in the fleet", and with nothing qualifying that, I have to assume the definite article means ALL SHIPS owned by the player using the ability.
This seems very powerful, but it also wipes out a planet's loyal population. Flavor-wise, the Nilari look creepy, so maybe there's a Deal with the Devil thing going on. Build a bunch of Transit Hubs for a deathtrap planet, and, when you win, you get a popup of The Nilari laughing at you for killing half the sentients in the sector.
But maybe it's not that powerful: According to https://strategywiki.org/wiki/Sins_of_a_Solar_Empire_II/Nilari_Cult, the ability only lasts 300s (still very good!), but it suggests the ability is best used when fighting over a planet you control:
>This ability is best used in a pitched defensive battle around one of your planets, especially if it is a high population planet such as a Terran or Desert planet. Triggering this around a highly populated planet can result in upwards of a +25% or higher bonus to weapon reload and ability recharge, allowing you to deal heavy damage to the opposing fleet.
Uh. What? Why wouldn't I use it when invading an enemy? Unless it only affects ships over the targeted planet? But that would be silly and inconsistent with the tooltip.
Bottom line: Is this buff permanent? Is there any limit to which ships are affected?