RTCs are pretty small and cheap. It's going to be much easier to add one to each set.
Furthermore, unless your chicken coop and your aquaponics are very close and you can install the two Arduinos at less than two meters from each other, I2C is pretty much out. Knowing the typical size of these installations I expect you're at much greater distance apart, which was also why I suggested multiple devices. Saves dealing with long wires on your sensors.