Hey, here is another cosmetic bug: if you obtain a neutronium source but not research "neutronium armor coating", the Empire Overview screen will show armor +7.5% bonus as if you have the tech. I think nothing else is affected - I've checked fleet overview (which appears when you click on a fleet), ship designer and ship armor value during combat. All of them correctly do not include bonus until you research the tech.
And I've just found another cosmetic bug on Empire Overview screen - the "diplomacy modifier" here does not account for leader traits. I have a leader with "empathic" trait and it does not reflect on the modifier at all. But it is reflected in alien's disposition when you communicate with them. The "infamous" trait is also not reflected in Empire Overview, but is accounted for in diplomacy screen.
And another cosmetic bug. On galaxy screen in left Overview panel click on "Strategic Resources" tab. If you have fully surveyed gas giants without helium-3 deposits, they will still be listed here with value 0.
Yes, it should only list the bonus if you have the tech. Thanks for reporting this, it will be fixed in the next update. The empire effects displayed in the empire overview screen are global empire-wide and more permanent in nature. Having the leader is not a permanent effect so that's why it's not listed. Yes, this is intended, it does list gas giants with 0 helium-3 deposits. There's still value to display those as they can be prime sites for constructing planets on, or to establish outposts to extend your supply range. If you wish to see gas giants with Helium-3 first you can sort by the amount of helium-3 present in the overview screen.