Something that just occurred to me: being placed in the Witness Protection program warrants a certain level of danger, as in
active. Personally, I'm not sure if they would place Akai's family in it just because he went undercover. Up until his cover was blown, there was no evidence that the BO suspected him. (Honestly, the BO seems strangely inefficient on background checks given how concise and careful they usually are.) As such, I think it's likely that they would be placed in the WP
after Akai's cover was blown, since there would be a high chance of retribution from the BO. However, even if this was done within an hour, the BO could probably manage to find out the rest of Akai's family, including some pictures of Masumi. Amuro would likely take heavy notice of this, since he's so obsessed with Akai, which is how he recognized her. Although, I don't think he's the kind of guy to kill people close to his enemies. I think he'd consider that kind of thing to be a bit of a cheap shot.
However, to be honest, I have serious doubts about the entire WP theory. I don't think they would let someone in it
go all the way to Japan, where her brother
died, and
where the very people they're protecting her from are based. Even if it was SOMEHOW deemed safe by the government for the family to leave the program, I don't think they'd let her go alone. Hell, her parents alone would raise giant objections of EPIC proportions. Even if they didn't know the full story, they'd have to know SOMETHING about why they were placed in the program. Just a generic "your son's cover was blown on an undercover mission in a very dangerous organization" would be enough to give them an idea of the danger. If she were to somehow hop a plane to Japan without their knowledge—especially AFTER their son got killed—they'd probably alert the government or some agent they know, and have her brought straight home. Also, transferring into a new school would undoubtedly require her parents' signatures or some other form of approval/consent. All in all, the WP just seems a bit too far-fetched for me. ...Unless her parents are absolute idiots (who pretty much miraculously gave birth to not one, but
two geniuses) or just don't care about their kids at all. ...Which could account for why she's so close to her loving older brother despite rarely seeing him.

But then again, that could work without adding in the WP.
Anyways, long story short, I just don't buy the WP idea because there's too many logic flaws. There was probably something done to protect the family, but just... I don't see the government letting her go to Japan so soon after her brother's death.
Also, I do have an idea for why she might know so much about Conan: she might be a fan girl. We've already seen one person blow a picture of him to poster-size, so why not have others? They could have met years ago at some beach-based case (thus why Ran associates her with the ocean), and the result of seeing him solve the case would leave a deep impression on her, leading her to follow his exploits. If it happened when they were kids, she would have a strong memory of Shinichi as a kid, since that would be the only time they met, and with her detective skills, this would make it even easier for her to recognize Conan as Shinichi. And Japanese fan girls
do have a certain reputation...
EDIT: Actually, the more I think about that last part, the more sense it makes. It explains why she's following him so much and lets him work with her as an equal. She's getting to live every fangirl's dream.