The bonus gained from city spells based on the number of essence is not updated once a scrying pool is built.
- City with 2 essence, spells Inspiration & Nature's Bounty cast and provide 2 research and 2 grain each (one per essence)
- Scrying Pool built: The bonus from Inspiration & Nature's bounty stay the same (+2)
- Spells canceled and cast again: The bonus is now 3 research and 3 grains, taking in account the new essence from the scrying pool.
I surmise that exiting the game and reloading the savegame may also be a workaround for this bonus refresh issue.