Belos probably cares for Hunter in a "pet raised for slaughter" kinda fashion.
Now, this isn't an exact analogy; the Emperor hasn't raised his nephew under inhumane conditions nor fully dehumanized him, even though the boy is an asset to him. A possible sacrifice too, seeing as Hunter is going to play a significant part in the "Titan's plans." And the Emperor won't hesitate; we are talking about a man who uses people however he sees fit in order to bring his ultimate goal into fruition.
Even I was never under the illusion that Hunter would ever take precedence over Belos' plans when I still thought he cared about his nephew as a person. Yet, Belos doesn't mind having Hunter around when he and the boy are discussing subjects relevant to Belos' interests – not Hunter's interests – or during his moments of vulnerability.
As if the kid is some kind of "trusted pet" who's there to serve his needs and commands, but not be heard.
Hunter's emotional needs? They matter less than his. Basically, this:
"It's nice having you around, Hunter. You're a trustworthy person." *Pats the kid's head like he's a dog.* "But please, can you not become an inconvenience? It's such a hassle, listening to your worries whilst dealing with my own. I hope you understand."
I know some people have compared Belos to Ghetsis, and the parallels are there, but at least Belos is genuinely friendly with his "pet." Ghetsis' Hydreigon hated him.
I don't think the Emperor's gonna turn out to be a complete monster.