Depends on the hotel. Certainly, a bad hotel will do nothing and pocket the money. A well-run hotel will actually do a deep cleaning of the room. That process is typically done by hotel staff.

Worst case scenario is having to hire outside people and/or equipment to clean the room. To do a proper removal of pet urine from carpet, you can't just spray some commercial cleaner and hope for the best. You really need to shampoo the carpet, which means you may have to take the room offline for a day to dry. In the hotel in which I worked, the cost of doing everything in this paragraph always cost more than the pet fee we took in for a single pet.

If hotels don't handle pet stains properly, they run the risk of making that room unsellable to anyone with a nose. Having to replace the carpet in one guest room can be very expensive unless the hotel happens to have spare carpet tucked away somewhere. Even if they do, it's unlikely that the replacement carpet will match the rest of the rooms. Although, that's more an aesthetics problem than a real one.