I'm working on SAAS project to which I just built an iOS interface. The service is not free, but the app client could be. Do I have to pay Apple when I charge the user for the service?
Only if you charge for the service through the app. Any purchase made in an app has to go through their in-app purchase system, which gives them a 30% cut. If they pay any other way (through a website for example) you're fine.
I'm fairly certain (but not absolutely certain) that there may be something in the Terms of Service about this. Otherwise many services could simply sell subscriptions or goods through a web interface and totally avoid any payment to Apple. Anyone whose read the TOS or otherwise can confirm?
You can't link to the SaaS purchase directly from the app. If you download Netflix or other services with an app, you will notice there is no option to sign up for the service within the app itself.