I don't understand why they're charging more per user as you scale. I don't know that I've ever seen a service like this.
More typical would be $12 per mo per agent from 1-3. $10 from 4-20, etc.
What's crazy is their service is considerably more expensive than hosted Exchange servers (which give you volume discounts, not increases) though Exchange probably costs a lot more to run. We use Zendesk and like it, but if we ever get to 20 or more support guys the business case for building our own ticketing system will be a slam dunk.