This is very possible because, quoting him, "Unlike you trainers, I don't consider Pokémon as friends. Unlike my fellow Team Galactic members, I don't treat them as tools. Instead, I make the power of Pokémon my own." So he doesn't really have any regard for his Pokémon, much less for his underlings. Or, he could've had Crobat before his transformation into an emotionless villain.
Cyrus is my favorite villain in the series (not counting N, I like N better but he's not a villain), because of how destructive he was and how far he went so that he could realize his plan. If there was a grade for "most evil" in the franchise, Cyrus would be at the highest level, IMO. The way he treated the Lake trio, no villain in the series had done such a cruel thing up to that point, and even beyond.
A number of things could've made him turn into the villain we knew. Infighting between his parents, who vented their frustrations at himself, could've made him retreat into reclusion, in the sole company of emotionless beings (machines). In a way, he had already created his own world as a child, where he was at the center, and he wanted to transpose his vision of the world to the rest of the universe when he became an adult and gained enough knowledge and power to do so.