No. Aptom couldn't kill them. He escaped.
The Libertus were designed by Hekering to rip hyper zoanoids apart. Aptom was outnumbered and they would have surely killed him. I have theorized that Agito wanted to have him killed and removed him from the playing field. Aptom is basically Sho's only super power support right now as Agito betrayed him.
Most if not all of them died fighting Guyot, Guyver 2F, and the Unus. Guyot wanted to take the Segowas hostage and hold them for a ransom, as I'm sure you can probably guess what for.
He's far from invincible. There's been many times he's had to retreat through out the manga and anime series.
Neo Zxtole almost killed him. Enzyme 3 almost killed him. Chronos is making stronger zoanoids that are inoculated against Aptom. He can't eat the newer types.
Eventually I wouldn't be surprised if Chronos vaccinated all zoanoids for a herd immunity against him. They're trying to phase him out and cut off his food supply.
It was never mentioned. But I wouldn't be surprised if Agito had them inoculated against Aptom.
We're talking about a guy who betrayed not only Sho but was a Chronos Collaborator through his Uncle. Agito isn't someone to be taken lightly and I don't think he's ignorant and unenlightened enough to have had them created knowing that Aptom could eat his super soldiers and cause him problems. No, Agito is smarter than that.
This is a guy who uses lateral thinking and forms of manipulation to get what he wants. He learns as much as he can and then comes up with ways to disarm and aggravate his enemies. Most of his plans are premeditated. The fall of the Japanese Branch was premeditated. He planned on them killing Sho and then used Sho to wreak havok on them while he worked in the shadows. This is also someone that took a lot of time planning Guyot's murder.
Agito has proven in the manga as well in the anime that he wants to rule the world in Chronos's place and he'll kill anyone that gets in his way including Sho. He's killed more zoalords than Sho has. He's done the most damage to Chronos. He's done a lot of covert operations against them. He's sabotaged them as much as he could when he was masquerading as a collaborator. He started a revolution. His superiority complex is what allowed him to temporarily commandeer Sho's Gigantic, especially when Sho was in battle. Perfect way to get Sho killed, which also sets the premise for Agito to deflect blame for his death.
He's a narcissistic sociopath who uses others to get what he wants and then he kills them after he's done. A lot of what sociopaths do is premeditated and they're very charming and convincing. He fooled Guyot until it got to a point that he was found out. He had been planning on screwing Guyot and Chronos over from the start of the story when he stole a Guyver unit and he did while his Uncle Genzo was director, who he screwed over. That's all he's done from the start is one power grab after the next and throwing people under the bus. If it gets him one step ahead, who cares.
When his plans fell apart after his cover was blown when he was scheming against Chronos. He resorted to puppeteering Sho until he was done with him & while doing so he formulated and meditated on different methods to screw them again. He sweet talked his followers, The Zeus Thunderbolt, and his girlfriend, Shizu, into becoming Libtertus after he kidnapped Hekering who was one of Chronos's greatest biologist. He doesn't care about Shizu. Only what she can do for him. With her and his super army he butchered thousands of zoanoids all for a pat on the back from a guy who is just as warped as Chronos is.
He's resourceful, he's ambitious, he's cunning, masterful in manipulating others, and he's power hungry. He's extremely intelligent. More so than Sho.
We're looking at a guy, a sociopath, whose desire is to get revenge and rule the world as a dictator. A guy who is willing to rule through a stratocracy and that often starts with an army and people giving them power which he has been given.
This isn't someone Aptom could win a fight with.