Fuuka didn't have to do any sneaky detective work. Honestly, she didn't really have to think much about it at all.
It had been nothing but a blessing when she had been accepted into SEES, no questions asked. For the first time in her life, she had friends. She had people who supported and cared for her, people who let her do as she pleased simply because it made her happy, people who protected her and trusted her to protect them in return.
Lucia allowed her to see the feelings of her companions. She would never tell them this, since she knew deep down that it was an unforgivable invasion of privacy, but it wasn't her fault that when she was using Lucia, she could not control what she saw of the humans nearby. Mitsuru's mind was always a whirlwind of lists, random facts and numbers that Fuuka couldn't hope to understand without years of study. Minato, Junpei, and Yukari were a swirl of stress from school, with a few added feelings of annoyance, fear, and anger. Koromaru was an enigma, likely because he didn't think in English. Aigis as well was inaccessible to Lucia's senses, and Ken was full of a lot more dark thoughts than Fuuka thought was healthy for such a young boy.
Akihiko though … Akihiko was, by far, the hardest human for Fuuka to read, and for the sake of curiosity, this made him the one on which she tried the hardest to do so. She could still feel his thoughts. In fact, she could practically taste them they were so close, but it was as if the older boy had put up a physical wall around his mind, protecting everything inside from the dangers of the world. Or was it that he was protecting the world from everything kept inside?
For months, Fuuka tried to read her senpai. She could feel the rumors about him, the opinions and the judgment from several other SEES members, but when it came to Akihiko's brain itself, only a heavy buzz escaped.
All this changed when Shinjiro first joined them.
There was still a wall around Akihiko's thoughts, but rather than it giving off the impression of a buzz, it was a soft hum. A warm hum, that filled Fuuka with a light happiness whenever Lucia picked up on it. Shinjiro, on the other hand, was a different story.
She had been asked from the beginning by Akihiko himself to keep an eye on Shinjiro when she could, making sure that he wasn't getting into trouble with shadows off in his alley. At the distance they were, she could only get a faint inkling of the feelings swirling through his mind, but what she could pick up on was dark and troubled, yanking down on her heart and mind until she was forced to pull away and focus on Akihiko for awhile, letting the monotone buzz numb her senses.
She had been expecting this on a much larger scale when Shinjiro joined the group. In fact, she had been terrified that she would be unable to use Lucia at all because of the strength of his negativity, so her surprise was immense when she summoned Lucia to feel a wave of calm serenity wash over her being, slow and sweet enough to nearly put her to sleep with the first wave. Pinpointing the source was easy, and she nearly fell over with the shock of it being Shinjiro. Shinjiro, who had seemed reluctant at first to return, but now that he had done so, also seemed to have no intention of leaving. Shinjiro, who had barely been able to step away from Akihiko for a moment since he had arrived. Shinjiro, who was, at that very moment, looking at Akihiko so strangely that Fuuka was horribly unsure on whether or not she was overstepping with her interpretation.
The combination of both Akihiko and Shinjiro's utter change in demeanor though sealed her theory as almost certainly correct. She just wished that she were brave enough to ask Mitsuru or Minato their opinions on the matter.
And that was how Fuuka knew.
A/N: Here's another instance of me probably taking a lot of liberties with headcanons when it comes to the workings and abilities of Fuuka's persona. I figured nothing was too out there though, but if there's anything that directly contradicts the FES canon, shoot me a message and I'll do my best to edit.