Pro II and Hysys are simulation software as you suspected. Correlations have been developed to predict the temperature, for a given pressure and composition, that hydrates will begin to form and those have been built into the programs. I believe, when I last talked to SimSci and Hysim that they felt these temperature predictions were within a degree of two (F) of the actual experimentally determined temperature. We used to use a margin of about 10F above the predicted hydrate temperature to allow for equation inaccuracies, data innacuracies and normal process variations in temperature/pressure/composition. I frankly don't remember if I ever ran both simulators on the same stream to see what the comparison in results were.
Both Pro II and Hysys (actually, I'm more familar with the older Hysim program) would develop a hydrate formation curve for any stream you wanted showing for each pressure, what the associated formation temperature was (Hysim was much easier IMO, the current version of Pro II supports getting a hydrate curve but in a completely bastardized method). Anyway, as long as you stayed above that temperature, hydrates wouldn't be a problem (knock wood). I know for Hysim (not sure about Hysys, the later version) that you could inject either glycol or methanol with a stream and it would predict the effect they would have on the hydrate formation temperature. Alternatively, you could use the GPSA method (Hammerschmidt).