Black and White in particular had the odd situation where I was playing as a super powerful god, but I seemed to spend all my time being a child minder to stupid minions.
Hmmm... I think that this is partly a problem of the player himself. Many players will try to optimize the game and doing all the stuff yourself will most likely always beat the gamelogic/AI. So, is the option to interact directly with your minions a desgin flaw ? It is similar to save games, once they are in, user will quick save/load through any challenge they encounter. But isn't the direct interaction with your minions one of difference to a pure simulation game (compare them to Sims or Settlers) ?
The problem with any resource management game is that it is very easy to add an F2P monitization strategy.
This might be true for the recent games (~5-7 years, or the newest installment of Dungeon Keeper) , but the lack of godmode games reaches back longer than F2P games.
I'd say Molyneux ran them to the ground by "overpromising" (aka, lying) for two decades.
Godus got "overpromised", B&W was "overhyped", nevertheless, most godgames were created by Molyneux , when ignoring direct clones.
I don't think god games have vanished, I think they've pretty much merged with sim city type games and RTS games. Look at Exiled, Reus, and Skyward collapse.
Maybe this is an identity problem. Looking at the games you have mentioned, or comparing Populus, Dungeon Keeper and Black & White, then all games are really different, it is even hard to define a core game mechanism. Comparing this to FPS or RTS games, you often have lot in common.
What have godgames in common ? I think, that godgames are often grounded in life-simulation, that the player as a god has some power to interact beyond being just a commander.