i know that my old apartment complex charge a $200 pet deposit, plus $50 for each additional pet (up to 2 pets per resident). my roommate had already paid the deposit for her pets before i got mocha and we both thought it would be ridiculous to pay another $200 just for mocha. i had told her i would pay her some of the deposit for her since we were flying under the radar with mocha, but she wouldn't take it.
i had mocha for 10 months out of our 12 month lease and was never caught. i would say since you already paid the deposit for your apartment, that's all you should pay.
is your apartment complex pet friendly, meaning that if you have guests over they can bring their pets over too? ours did, and it was really hard to tell if they were mine or my guests.
i hope it works out for you.