Local shop here in IN charges $40 to program a radio, no matter if it's mobile or handheld. That's $40 flat rate, doesn't matter how many channels or zones. Think of zones like banks. Bank 1 holds 16 channels, bank 2 can hold 16 more channels, etc... Kind of like on a car stereo where you have FM1 and FM2.
My department actually ended up just buying the software and cables to program all of our radios ourselves, figuring we would spend $1000 easily in the next two years reprogramming new and used radios for switch channels that are no longer used and for narrowbanding.