We knew to expect rock (limestone) right under the surface when we dug our pool. What we didn't know is if we'd hit the "blue rock" under the limestone that is even harder to get through. The excavators around here charge a base price for the pool depending on its size, then an hourly rate (typically $250/hour) once they need to start using the rock hammer. The guy I went with instead charged by the volume of rock he had to haul off, which was a more definite amount based on the pool size instead of an open ended amount of time, and I liked that. He was actually the excavator I felt was the most experienced and the one I had most confidence in, so that helped too. In the end, though, if I were to have calculated the hours vs the price for what he had to haul off, it worked out pretty comparable, since we did end up hitting the blue rock and it was very very hard and took a long time to get through.
The cost of excavation was pretty steep for us because of the rock, but there was no getting around it, and we factored it into our budget. The hard part is the not knowing so not being able to budget well, but we knew what to expect and had a worse case scenario factored into our budget.
One thing I also had to consider was what to do with the rock. Since we were O/B and my excavator wasn't local to my area, he wasn't familiar with where to dump it. Supposedly it's easy to find people who want good fill dirt, but not everyone wants your rock! If you have a PB then they will figure that out for you, but I had at least one excavator that didn't want to deal with me because it was too much trouble figuring out what to do with the rock. My excavator said he'd call around, but I decided to be proactive and tracked down my own place to dump sooner than he probably would have gotten to it. It all worked out in the end, fortunately.
Good luck! I hope for your sake all the rocks in your area decided to take up residence in your neighbors' yards instead of yours! ;-)