Yes, I think part of her would be thankful. I'm pretty sure Shiho and Akai have met before, but dunno when or how. They're probably just acquaintances, not friends. I don't think she still considers Akai to be part of the BO (Conan would've cleared it up with her), but I think she is wary and slightly suspicious of him, perhaps because he was the cause of her sister's death. Of course, if she was thankful to him, this might be down toned slightly. It's likely that perhaps when she saw Akai on the bus, she thought he was still part of the BO (at that time).