Below are mods that add such a mechanism.
GoldenAge - Brave New World (comprehensive overhaul mod)
https://steamcommunity.com/sharedfiles/filedetails/?id=2209309479
The more cities a civilization owns, the lower its output per city.
This penalty can be erased by increasing the population per city.
This encourages the development of large cities rather than spamming small cities.
Colony and Empire (comprehensive overhaul mod / created by me)
https://steamcommunity.com/sharedfiles/filedetails/?id=2628959632
The more cities a civilization owns, the lower its output and loyalty per city.
This penalty can be mitigated by adopting a more advanced government.
This will curb the rapid expansion of civilization in the early stages of the game.
Strudeler's Civilization VI Deluxe (comprehensive overhaul mod)
https://steamcommunity.com/sharedfiles/filedetails/?id=2493022278
Wide and Tall Play changes:
All Cities after the Capital incur an additional -1% Science and Culture as well as a -2% Gold and Faith penalty per City (stacking up to -25%/50% at 25 Cities).
Key Loyalties (small mod)
https://steamcommunity.com/sharedfiles/filedetails/?id=2003092025
The more cities a civilization owns, the lower the maximum loyalty per city.
In addition, the city's output is reduced according to the maximum value of loyalty.