No, it doesn't emulate, more like interpreting the extra features of the CD32 AFAIK.
But, yes, it does use WinUAE as it's basis (which leads you to my third paragtraph
), and not having looked at akiko since the day after it was originally released it uses an old version of WinUAE before Toni even took over.
At the end of the day, akiko is an illegal project in my eyes. Not that I know much about licensing or anything like that, but UAE is under some GNU license meaning every version of any program that uses it's code should be free (I think). So that's why I think akiko is pap, the fact that WinUAE is 1000x better at emulating a CD32 is secondary