I really don't believe Akai's dead. Have you seen Conan's smile
when Eisuke told him, that the FBI's mood is down since someone
seemed to have died?
Since I don't know if there's a spoiler funkction, I'm warning you,
before you read the following lines.
I'm quite shure, Akai's the graduate student that now lives
in Shinichi's house. Why else should Conan have offered his own
house to him? He also makes some comments about colours in the
burned house case ("I hate black", he's the "red" guy: akai = red)
And his comments about Holmes, it's almost as if
they arranged that as a sign for each other.
You don't actually see the head shot and Akai's body changes its
position when he lies inside the car (watch his head!). I think, he took
that other BO Agent who was in the hospital and killed himself (per head shot^^) and swapped places with his corpse.
The funny thing is, that Gin himself ordered the headshot^^
If he hadn't ordered this, it would be very suspicious to find a man who was
killed by a headshot. But since the corpse and Akai are supposed to have a whole
up there, Gin actually tricked himself^^