Generally, if what you have right now is legal, they would be grandfathered in. They can and often do add stipulations, though. Such as you may not be allowed to add more animals. Or you might not be allowed to replace any animals that die with new ones. Those type of decisions will come down to...
Grandfathering means that if they rezone where you live, or change an ordinance, as long as you lived there before the changes, they may not make you follow the new rules. For example let's say you have 30 chickens in your agricultural zone property right now. But the city annexes your property...