Since the show executed this part so poorly, I'd even assume that Miri doesn't know everything. She certainly knows that mom's dead, the way she talked with the picture. But, the dads may have only told her half-truth. For example, they could've said that mom had cancer and didn't want Miri to see her die so she left her and died peacefully somewhere far away or something, entrusting Miri to the two.
I can't imagine Miri being just as energetic and happy (on pictures too) knowing her mom was killed in their apartment, in cold blood. That dad's are assassins who killed her real father and are responsible for her real mom's death too!
There's no real evidence to support the opposite. You could say she knows everything and is still fine with it - realism be damned.
Honestly hard to say. I think that as a child she didn't know. But as a high school girl, I think there is such a possibility, since they said to her as a child that her mother went for a long trip, and long trip can last so much - Miri became high school girl, so she probably asked about her mother again, but what Rei and Kazuki told her is hard to say. As for her father, I think they are quiet about it, since they promised to protect her and there is no reason to tell and hurt her that they killed her father who was with mafia.
1. Miri found out the truth when she grew older with Kazuki and Rei telling her everything. It's possible she accepted the fact they had killed her biological father as since she was a child, her definition of a father was 'someone who protects' her, and so she had already recognised Kazuki and Rei to be her fathers. Her mother being killed and both dads being killers may not come as a surprise to her afterall she had personally witnessed a gunfight as a child, and had absolutely no reaction. When she grows older, the gunfighting may be something she remembers, and so the truth probably won't be that much of a shocker after careful thinking on her part.
2. Miri never finds out the truth, and Kazuki and Rei basically shields her from all the dirty secrets. Miri may have forgotten all her memories as a child (not sure how old she was at the start of the anime), but it's possible her memories of gunfights are completely wiped. Kazuki and Rei would've continued running their restaurant business and the truth would never have come to light. Miri should've noticed her mother's death sometime after the end of the anime as she talked to the picture of her mother, but K&R might not have told her the true reason of her death.
Personally I would prefer the first possibility, afterall its not good to have such deep secrets within a family. And I do believe Miri would come to terms with it without significant difficulties, even though she may be shocked and disappointed for a period of time.