Using Ammonia to control the pH works fine and is standard practice in many installations. Problems which have been experienced relate to salt deposition. Design and position the injection quills properly and you should be fine.
I'm not sure which of the tailgas processes you are trying to model. I am familiar with the SCOT process. You can model the process on HYSYS. The amine section is a challenge without the amine add-in on HYSYS but can be done. The HYSYS model is pretty detailed.
If you are comparing processes...