It is hard to say what is eating your petunias, but rabbits could definitely be the culprit since you know they are around. If you can find a stem that was eaten, see if the bite was taken at a 45-degree angle, which would indicate a rabbit.
Chipmunks are also known to eat flowers. It is probably not birds, or you would see beak-shaped rips in some.
As for using eggshells as a repellent, it is not the eggshells that repel but the degradation of the proteins in the egg residue on the shells. There are commercial repellents, proven in peer-reviewed literature, based on this process of protein degradation (Deer-Away, Big Game Repellent). These should be appropriate for rabbits as well. Be aware, as with all repellents, that hunger often overrides bad taste or fear.
Online Resources:
Cottontail Rabbit Control