My county's fees are the same way...not as high, but unaltered are higher $24 rather than $12. I think you'd be amazed at how many people probably neuter/spay because they do want to register a pet and get the "discount." Many people are oblivious, they don't know how/why they could get caught, so they'll register, and when they see that the fees are less, they'll spueter. IMO...due to the pet population, if it gets just one more person to speuter, its worth it. And if you decide not to, and you license, well then you're providing income to Animal Control which is also useful.
I know for a fact that most dogs in our county aren't registered...I live in Milwaukee and I registered in April last year (day before the deadline) and I had tag number 49XX...so no where near the true amount of pets in the county.
You do get some things in our city other than your dog is then registered with animal control so if its picked up, and is wearing its tag, they can look up your information and get the dog back to you (if you don't have a microchip). You're also not allowed to purchase a license to the county's dog parks without one...even though I'm sure the majority of people don't buy those either and still go to the dog parks.