Well one theory could go like this. They were genetically engineered correct? Well what if the Masters had devised away to alter the chemicals in the brain of the clone/Zentradi to obey? But like in all things in nature, things evolve or adapt to their environment under certain conditions and/or stresses. I won't go any further than that as it gets to personal with me.
Or quite simply most of them did not live long enough to learn any different.
Or if you keep their mentality on a child like level they will always be dependent upon leadership to guide them and make decisions for them. Given the observations of most of the common soldiers behavior in the episodes I would believe this to be the rule and the types like Breetai, Exadore, and Dolza the exception to that fact. They were just lucky enough to survive the many fights and battles. Perhaps that is how the leaders and commanders of the Zentradi were "Naturally" selected?
But I believe that their genes would not be used for recloning as they would produce a "TOO" intelligent soldier. The Masters were just that Masters of cloning humans via
Protoculture with the traits they desired to serve them i.e. bioroid pilots, musicians etc...
So I believe it was short life span with a child like mentality and an overall fear of their master because of the secrecy behind the power of protoculture the masters held over their minions heads.
I don't think it would get any clearer than that. No mind control here, maybe psychology, but not mind control.