It makes more sense to exclude unfertilized eggs from the hatch rate calculations, since they were never going to hatch anyway. They'd just muddy the statistics. That's why breeders keep track of "fertility rate" as a separate variable. Because you are measuring two different things. At the first stage of checking for development and weeding out, you toss the unfertilized eggs, do the math and end up with the fertility rate (how well the lovin' is going). You proceed only with the fertilized eggs - the ones that have a chance at hatch - to measure the hatch rate. From that point on, whoever makes it to hatch enters the statistics and you have the actual hatch rate.
It makes more sense to measure fertility rate and hatch rate separately so if there's a problem, you'd know where it is. If you set 10 eggs but only 3 hatch, that might look like a poor hatch rate, but if you break it down and see that those 7 weren't fertilized at all, then everything changes. Now you have a great hatch rate, and a rooster who needs to step it up. Alternatively, if all 10 started developing but 7 died prematurely, then your problem is with the eggs themselves, or with the broody, or your incubator, etc. - problem is elsewhere entirely. So if you were selling eggs for hatching, for example, you'd need to track those variables separately, so you'd know if the turnout was poor, if it was your fault or your buyer's fault. Breeders need to check fertility rates periodically and have a general idea of how the flock is doing, and provide that information to the buyer. Then the buyer tracks the hatch rate once they set the eggs.
I've had both extremes happen to me. A batch of shipped eggs with 100% fertility rate, but only 50% hatch rate (because they were shipped and jostled). Or a batch of local eggs that had 20% fertility rate, but 100% hatch rate. If you don't look at the two rates separately, but only at how many eggs out of the total hatched, it would look like the shipped eggs did better - they had a better "hatch rate" of 50%, while the local eggs only had a 20% success. But that's not true at all. The local eggs produced fewer chicks, but only because the rooster was young and not doing the job well enough yet. Every single egg that was fertilized, made it to hatch - 100% hatch rate. Whereas with the shipped eggs, the rooster did great and all eggs had potential, but only half of them made it - so half the hatch rate of the local eggs. Local eggs win the hatch rate contest, even though they produced fewer chicks.