This makes me wonder how exactly a clone is any different from an identical twin, because Yamato and Maru don't look as alike as I was expecting. Aside from Maru obviously being smaller due to malnourishment, their eyes, nose and even face shapes all look different; I'd say Yamato resembles grown up Kona a bit more while Maru resembles tween Tokio.
I don’t what you’re on about, Yamato’s eye, nose, and face shapes look identical to Maru’s.
But to answer your question, in real-life, clones created in labs may have different mitochondrial DNA than the original, depending on the source of the ovum used to create the clone, but I expect that wouldn’t be issue for an being like Mīna in this science-fiction story.
But yes, a clone that also has the same mitochondrial DNA is functionally the same thing as an identical twin.
The first guy must actually be Tokio, she's posing as Yamato in front of visitors to protect her son from assassination attempts because she knows Yamato can kill kirukos and that puts him in danger. That's why she got the "medicine" in lieu of Yamato, because it's made to kill the person who can get rid of Meena's children. The little blonde kid must be her grandchild and Yamato's child.
As far as we know, Tokio has no means to know about the purported effects of the “medicine”, so I doubt she took it specifically because she was aware of its effects. She could definitely be suspicious in general though.
Though she could also be interested if it has any effect on her specifically since Maru’s words at that specific were only about giving medicine to a person with the same face as him, and Tokio also looks almost identical to her sons.