Quatuanary ammonias are MUCH MUCH more effective than chlorhexadine. Way overboard in my opinion, but in a zoo or rescue setting, quarantine and sick animals are much more likely to come up, thus the extra protection.
Chlorhexadine (acetate or gluconate) is much less nautious, and although all disinfectants should be rinsed well, if Ch. does get on an animal, it's of no concern.
I use quat's for my boas (unfortunately I have an IBD quarantine scenerio happening), but nothing for my happy and healthy herps within my collection. Chlor. is used on occasion if a cage is a real mess; but more for it's soap-like qualities.
Hope this proves informative 
Ian