Could root canal treatments substantially decrease the chance of having endodontic cysts?

Definitely: Endodontic infections fall into two categories, "granulomas" which comprise ~95%, and "cysts" which comprise ~5% of endodontic infections. Root canal treatments are performed in order to prevent or heal endodontic infections. If you don't have an endodontic cyst, having a root canal treatment definitely decreases the chance of having endodontic cysts.

Yes: Properly performed root canals should not cause cysts. If they do, then the tooth can be retreated, or have a surgical procedure at the tip of the root to clear up the abscess.